Refactor config

.github/workflows/_run_tests.yml

@@ -34,6 +34,11 @@ jobs:
     - name: Conda info
       shell: bash -l {0}
       run: conda info
+    - name: Install mono
+      shell: bash -l {0}
+      run: |
+        conda install mono
+
     - name: Perform pip installation with all stable dependencies
       shell: bash -l {0}
       run: |

alphadia/constants/default.yaml

@@ -1,6 +1,11 @@
 # configuration for the extraction plan
 version: 1
 
+library: null
+output_directory: null
+raw_path_list: []
+output: null
+
 general:
   thread_count: 10
   # maximum number of threads or processes to use per raw file
@@ -26,7 +31,7 @@ library_prediction:
   variable_modifications: 'Oxidation@M;Acetyl@Protein_N-term'
   max_var_mod_num: 2
   missed_cleavages: 1
-  precursor_len:
+  precursor_len: # TODO: make this min/max ?
     - 7
     - 35
   precursor_charge:
@@ -53,6 +58,9 @@ library_prediction:
 
 # define custom alphabase modifications not part of unimod or alphabase
 # also used for decoy channels
+# TODO make this a list
+#  - name: Dimethyl:d12@K
+#    composition: H(-2)2H(8)13C(2)
 custom_modifications:
   # Dimethyl @K channel decoy
   Dimethyl:d12@K:
@@ -191,8 +199,12 @@ library_multiplexing:
   # channels can be either a number or a string
   # for every channel, the library gets copied and the modifications are translated according to the mapping
   # the following example shows how to multiplex mTRAQ to three sample channels and a decoy channel
+  # TODO make this a list
+  #    - channel_name: 0
+  #      channel_modifications:
+  #        mTRAQ@K: mTRAQ@K
+  #        mTRAQ@Any_N-term: mTRAQ@Any_N-term
   multiplex_mapping: {}
-
     #0:
     #  mTRAQ@K: mTRAQ@K
     #  mTRAQ@Any_N-term: mTRAQ@Any_N-term
@@ -373,11 +385,12 @@ transfer_learning:
   # instrument type encoded during training
   instrument: 'Lumos'
 
+
 # configuration for the calibration manager
 # the config has to start with the calibration keyword and consists of a list of calibration groups.
 # each group consists of datapoints which have multiple properties.
 # This can be for example precursors (mz, rt ...), fragments (mz, ...), quadrupole (transfer_efficiency)
-calibration_manager:
+calibration_manager: # TODO move to a separate file or hard-code
   - name: fragment
     estimators:
       - name: mz

alphadia/search_step.py

@@ -134,7 +134,7 @@ def _init_config(
             extra_config["output"] = output_folder
             config_updates.append(extra_config_update)
 
-        config.update(config_updates, print_modifications=True)
+        config.update(config_updates, do_print=True)
 
         if "output" not in config:
             config["output"] = output_folder