Removed commented out sections of code

OSOceanAcoustics · Sep 25, 2024 · 9b01efc · 9b01efc
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commit 9b01efc
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diff --git a/config_files/initialization_config.yml b/config_files/initialization_config.yml
@@ -45,20 +45,7 @@
     file_columns: [transect_num, region_id, vessel_log_start, vessel_log_end, latitude, longitude,
                    stratum_num, transect_spacing, layer_mean_depth, layer_height, bottom_depth,
                    NASC, haul_num]
-  # haul_to_transect_mapping:
-  #   save_file_template: "haul_to_transect_mapping_{YEAR}_{COUNTRY}"
-  #   country_code: [CAN, US]
-  #   file_settings:
-  #     US:
-  #       directory: /Biological/US
-  #       sheetname: Sheet1
-  #     CAN:
-  #       directory: /Biological/CAN
-  #       sheetname: Sheet1
   transect_region_mapping:
-    # save_file_template: "{COUNTRY}_{YEAR}_transect_region_haul_{GROUP}.xlsx"
-    # save_file_directory: /Stratification
-    # save_file_sheetname: Sheet1
     pattern: "{REGION_CLASS}{HAUL_NUM}{COUNTRY}"
     parts:
       REGION_CLASS:

diff --git a/config_files/survey_year_2019_config.yml b/config_files/survey_year_2019_config.yml
@@ -43,14 +43,6 @@ biological:
     CAN:
       filename: Biological/CAN/2019_biodata_catch_CAN.xlsx
       sheetname: biodata_catch_CAN
-  # haul_to_transect:
-  #   US:
-  #     # filename: Biological/US/haul_to_transect_mapping_2019_US.xlsx
-  #     filename: Biological/US/haul_to_transect_mapping_2019.xlsx
-  #     sheetname: Sheet1
-  #   CAN:
-  #     filename: Biological/CAN/haul_to_transect_mapping_2019_CAN.xlsx
-  #     sheetname: Sheet1
 stratification:
   strata:
     # The two stratification types are found in two sheets: "Base KS" and "INPFC"
@@ -64,38 +56,25 @@ NASC:
   # NASC values
   no_age1:
     # file that excludes age1 values
-    # filename: Exports/US_CAN_detailsa_2019_table2y+_ALL_final - updated.xlsx
-    # filename: Exports/US_CAN_detailsa_2019_table2y+_ALL_final - updated.xlsx
     filename: Exports/US_CAN_NASC_2019_table_no_age1_test.xlsx
     sheetname: Sheet1
   all_ages:
     # file that includes all ages
-    # filename: Exports/US_CAN_detailsa_2019_table1y+_ALL_final - updated.xlsx
-    # filename: Exports/US_CAN_detailsa_2019_table1y+_ALL_final - updated.xlsx
     filename: Exports/US_CAN_NASC_2019_table_all_ages_test.xlsx
 
     sheetname: Sheet1
 export_regions:
   all_ages:
-    # filename: Stratification/US_CAN_2019_transect_region_haul_age1+ auto_final.xlsx
     filename: Stratification/CAN_US_2019_transect_region_haul_all_ages.xlsx
     sheetname: Sheet1
   no_age1:
     filename: Stratification/CAN_US_2019_transect_region_haul_no_age1.xlsx
     sheetname: Sheet1
-# gear_data:
-#   US:
-#     filename: Biological/US/2019_biodata_gear.xlsx
-#     sheetname: biodata_gear
-#   CAN:
-#     filename: Biological/CAN/2019_biodata_gear_CAN.xlsx
-#     sheetname: biodata_gear_CAN
 kriging:
   mesh:
     filename: Kriging_files/Kriging_grid_files/krig_grid2_5nm_cut_centroids_2013.xlsx
     sheetname: krigedgrid2_5nm_forChu
   isobath_200m:
-    # filename: Kriging_files/Kriging_grid_files/Smoothing_EasyKrig.xlsx
     filename: Kriging_files/Kriging_grid_files/transformation_isobath_coordinates.xlsx
     sheetname: Smoothing_EasyKrig
   vario_krig_para:

diff --git a/echopop/core.py b/echopop/core.py
@@ -164,7 +164,6 @@
             "vessel_log_end": np.float64,
             "latitude": np.float64,
             "longitude": np.float64,
-            # "stratum_num": int,
             "transect_spacing": np.float64,
             "NASC": np.float64,
             "haul_num": int,
@@ -176,7 +175,6 @@
             "vessel_log_end": np.float64,
             "latitude": np.float64,
             "longitude": np.float64,
-            # "stratum_num": int,
             "transect_spacing": np.float64,
             "NASC": np.float64,
             "haul_num": int,

diff --git a/echopop/survey.py b/echopop/survey.py
@@ -149,9 +149,6 @@ def load_survey_data(self, verbose: bool = True):
             Console messages that will print various messages, updates, etc. when set to True.
         """
 
-        # Create haul-transect-mapping key file
-        # el.write_haul_to_transect_key(self.config, verbose)
-
         # Get previously processed datasets
         # ---- Updated datasets
         new_datasets = ["biological", "kriging", "stratification"]

diff --git a/echopop/utils/load.py b/echopop/utils/load.py
@@ -610,10 +610,6 @@ def prepare_input_data(input_dict: dict, configuration_dict: dict):
     if set(["biology", "spatial"]).issubset(imported_data):
 
         # Merge haul numbers and spatial information across biological variables
-        # ---- Consolidate information linking haul-transect-stratum indices
-        # input_dict["biology"]["haul_to_transect_df"] = input_dict["biology"][
-        #     "haul_to_transect_df"
-        # ].merge(input_dict["spatial"]["strata_df"], on="haul_num", how="outer")
         # ---- Create interval key for haul numbers to assign INPFC stratum
         haul_bins = np.sort(
             np.unique(
@@ -655,28 +651,6 @@ def prepare_input_data(input_dict: dict, configuration_dict: dict):
                 )
                 # ---- Reset the index
                 input_dict["biology"][keys].reset_index(inplace=True)
-        # ---- Define haul bins with `haul_to_transect_df`
-        # input_dict["biology"]["haul_to_transect_df"]["haul_bin"] = pd.cut(
-        #     input_dict["biology"]["haul_to_transect_df"]["haul_num"], haul_bins
-        # )
-        # ---- Define INPFC stratum for `haul_to_transect_df`
-        # input_dict["biology"]["haul_to_transect_df"] = input_dict["biology"][
-        #     "haul_to_transect_df"
-        # ].merge(input_dict["spatial"]["inpfc_strata_df"][["stratum_inpfc", "haul_bin"]],
-        # how="left")
-        # ---- Distribute this information to other biological variables
-        # -------- Specimen
-        # input_dict["biology"]["specimen_df"] = input_dict["biology"]["specimen_df"].merge(
-        #     input_dict["biology"]["haul_to_transect_df"], how="left"
-        # )
-        # # -------- Length
-        # input_dict["biology"]["length_df"] = input_dict["biology"]["length_df"].merge(
-        #     input_dict["biology"]["haul_to_transect_df"], how="left"
-        # )
-        # # -------- Catch
-        # input_dict["biology"]["catch_df"] = input_dict["biology"]["catch_df"].merge(
-        #     input_dict["biology"]["haul_to_transect_df"], how="left"
-        # )
 
     # ACOUSTICS + SPATIAL + BIOLOGICAL
     if set(["acoustics", "biology", "spatial"]).issubset(imported_data):

diff --git a/echopop/utils/validate.py b/echopop/utils/validate.py
@@ -135,14 +135,6 @@ def validate_type(value: Any, expected_type: Any) -> bool:
         item_type = expected_type.__args__[0]
         return all(validate_type(item, item_type) for item in value)
 
-    # # Handle numpy.ndarray
-    # if hasattr(expected_type, "__origin__") and expected_type.__origin__ is np.ndarray:
-    #     return (
-    #         isinstance(value, np.ndarray)
-    #         and np.issubdtype(value.dtype, np.number)
-    #         # and value.dtype == np.float64
-    #     )
-
     return False