Merge backwards compatibility #346

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Merged

brandynlucca merged 54 commits into OSOceanAcoustics:main from brandynlucca:main

Apr 29, 2025

.codespell-ignore-words.txt

-Original file line number
+Diff line change
@@ Expand Up / @@ -2,3 +2,4 @@ Calss @@
     calss
     Tranect
     tranect
+    notin

.pre-commit-config.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,9 @@ exclude: | @@
       (?x)^(
         echopop/test_data/|
         docs/|
-        project_docs
+        project_docs|
+        echopop/file_investigation.py|
+        echopop/test_survey.py
       )
     repos:
       - repo: https://github.com/pre-commit/pre-commit-hooks
@@ Expand Down @@

config_files/initialization_config_2011.yml

-Original file line number
+Diff line change
@@ -0,0 +1,107 @@
+    # This YAML file is a configuration file for all
+    # initialization parameters used in Echopop
+    ---
+      #####################################################################################################################
+      # Survey data processing#
+      ########################
+      # Jolly and Hampton (1990) stratified mean calculation
+      stratified_survey_mean_parameters:
+        strata_transect_proportion: 0.75                          # percent of Jolly-Hampton transects in each stratum
+        num_replicates: 10000                                     # number of resample replicates
+        mesh_transects_per_latitude: 5                            # number of virtual transects per degree latitude in kriging mesh
+      #####################################################################################################################
+      # Biological data processing#
+      ########################
+      # Jolly and Hampton (1990) stratified mean calculation
+      bio_hake_len_bin: [                   # length sequence array 2 - 80 cm. This specifies the bin centers!
+,                    # start of bin centers
+,                   # end of bin centers
+# number of bins in total
+      ]
+      bio_hake_age_bin: [                   # age sequence array: year - age  1-22
+,                    # start of sequence
+,                   # end of sequence
+# number of points in the sequence
+      ]
+      #####################################################################################################################
+      # Acoustic transect export processing#
+      ########################
+      nasc_exports:
+        export_file_directory: /raw_nasc
+        nasc_export_directory: /Exports     # Acoustic export directory
+        save_file_template: "{REGION}_NASC_{YEAR}_table_{GROUP}.xlsx"
+        save_file_sheetname: Sheet1
+        regions:                            # Main acoustic data region names (list or single string)
+          all_ages: [Age-1 Hake,            # Age-1+
+                      Age-1 Hake Mix,
+                      Hake,
+                      Hake Mix]
+          no_age1: [Hake, Hake Mix]         # Age-2+
+        max_transect_spacing: 10.0          # Maximum transect spacing (nmi)
+        file_columns: [transect_num, region_id, distance_s, distance_e, latitude, longitude,
+                        stratum_num, transect_spacing, layer_mean_depth, layer_height, bottom_depth,
+                        NASC, haul_num]
+      transect_region_mapping:
+        parts:
+          REGION_CLASS:
+            - pattern: ^[hH](?![a-zA-Z]|1a)
+              label: Hake
+            - pattern: ^[hH]1[aA][mM]
+              label: Age-1 Hake Mix
+            - pattern: ^[hH]1[aA]
+              label: Age-1 Hake
+            - pattern: ^[hH][mM]
+              label: Hake Mix
+            - pattern: hake_mix
+              label: Hake Mix
+            - pattern: hake
+              label: Hake
+          HAUL_NUM:
+            - pattern: '[0-9]+'
+              label: None
+          COUNTRY:
+            - pattern: ^[cC]
+              label: CAN
+            - pattern: ^[uU]
+              label: US
+        pattern: "{REGION_CLASS}{HAUL_NUM}{COUNTRY}"
+        inpfc_strata_region:
+          CAN: [6]
+          US: [1, 2, 3, 4, 5]
+        save_file_template: "{COUNTRY}_{YEAR}_transect_region_haul_{GROUP}.xlsx"
+        save_file_directory: /Stratification
+        save_file_sheetname: Sheet1
+      #####################################################################################################################
+      # Log-linear regression#
+      ########################
+      # Target strength (TS) - length (L) regression: TS=m*log10(L)+b
+      TS_length_regression_parameters:
+        pacific_hake:                         # corresponding species text code
+          number_code: 22500                  # species number code
+          TS_L_slope: 20.0                    # the 'm' or 'slope' parameter
+          TS_L_intercept: -68.0               # the 'b' or 'y-intercept'
+          length_units: cm                    # units for L used in regression/relationship
+      #####################################################################################################################
+      # Geospatial settings#
+      ########################
+      geospatial:
+        init: epsg:4326                       # EPSG integer code for geodetic parameter dataset
+      #####################################################################################################################
+      # Kriging parameters#
+      #####################
+      kriging_parameters:
+        A0: 6.25                              # base area of the grid cell
+        longitude_reference: -124.78338       # longitude reference for kriging mesh adjustment
+        longitude_offset: -124.78338          # longitudinal offset for kriging mesh adjustment
+        latitude_offset: 45.0                 # latitudinal offset for kriging mesh adjustment
+      #####################################################################################################################
+    ...

config_files/initialization_config_2012.yml

-Original file line number
+Diff line change
@@ -0,0 +1,107 @@
+    # This YAML file is a configuration file for all
+    # initialization parameters used in Echopop
+    ---
+      #####################################################################################################################
+      # Survey data processing#
+      ########################
+      # Jolly and Hampton (1990) stratified mean calculation
+      stratified_survey_mean_parameters:
+        strata_transect_proportion: 0.75                          # percent of Jolly-Hampton transects in each stratum
+        num_replicates: 10000                                     # number of resample replicates
+        mesh_transects_per_latitude: 5                            # number of virtual transects per degree latitude in kriging mesh
+      #####################################################################################################################
+      # Biological data processing#
+      ########################
+      # Jolly and Hampton (1990) stratified mean calculation
+      bio_hake_len_bin: [                   # length sequence array 2 - 80 cm. This specifies the bin centers!
+,                    # start of bin centers
+,                   # end of bin centers
+# number of bins in total
+      ]
+      bio_hake_age_bin: [                   # age sequence array: year - age  1-22
+,                    # start of sequence
+,                   # end of sequence
+# number of points in the sequence
+      ]
+      #####################################################################################################################
+      # Acoustic transect export processing#
+      ########################
+      nasc_exports:
+        export_file_directory: /raw_nasc
+        nasc_export_directory: /Exports     # Acoustic export directory
+        save_file_template: "{REGION}_NASC_{YEAR}_table_{GROUP}.xlsx"
+        save_file_sheetname: Sheet1
+        regions:                            # Main acoustic data region names (list or single string)
+          all_ages: [Age-1 Hake,            # Age-1+
+                      Age-1 Hake Mix,
+                      Hake,
+                      Hake Mix]
+          no_age1: [Hake, Hake Mix]         # Age-2+
+        max_transect_spacing: 10.0          # Maximum transect spacing (nmi)
+        file_columns: [transect_num, region_id, distance_s, distance_e, latitude, longitude,
+                        stratum_num, transect_spacing, layer_mean_depth, layer_height, bottom_depth,
+                        NASC, haul_num]
+      transect_region_mapping:
+        parts:
+          REGION_CLASS:
+            - pattern: ^[hH](?![a-zA-Z]|1a)
+              label: Hake
+            - pattern: ^[hH]1[aA][mM]
+              label: Age-1 Hake Mix
+            - pattern: ^[hH]1[aA]
+              label: Age-1 Hake
+            - pattern: ^[hH][mM]
+              label: Hake Mix
+            - pattern: hake_mix
+              label: Hake Mix
+            - pattern: hake
+              label: Hake
+          HAUL_NUM:
+            - pattern: '[0-9]+'
+              label: None
+          COUNTRY:
+            - pattern: ^[cC]
+              label: CAN
+            - pattern: ^[uU]
+              label: US
+        pattern: "{REGION_CLASS}{HAUL_NUM}{COUNTRY}"
+        inpfc_strata_region:
+          CAN: [6]
+          US: [1, 2, 3, 4, 5]
+        save_file_template: "{COUNTRY}_{YEAR}_transect_region_haul_{GROUP}.xlsx"
+        save_file_directory: /Stratification
+        save_file_sheetname: Sheet1
+      #####################################################################################################################
+      # Log-linear regression#
+      ########################
+      # Target strength (TS) - length (L) regression: TS=m*log10(L)+b
+      TS_length_regression_parameters:
+        pacific_hake:                         # corresponding species text code
+          number_code: 22500                  # species number code
+          TS_L_slope: 20.0                    # the 'm' or 'slope' parameter
+          TS_L_intercept: -68.0               # the 'b' or 'y-intercept'
+          length_units: cm                    # units for L used in regression/relationship
+      #####################################################################################################################
+      # Geospatial settings#
+      ########################
+      geospatial:
+        init: epsg:4326                       # EPSG integer code for geodetic parameter dataset
+      #####################################################################################################################
+      # Kriging parameters#
+      #####################
+      kriging_parameters:
+        A0: 6.25                              # base area of the grid cell
+        longitude_reference: -124.78338       # longitude reference for kriging mesh adjustment
+        longitude_offset: -124.78338          # longitudinal offset for kriging mesh adjustment
+        latitude_offset: 45.0                 # latitudinal offset for kriging mesh adjustment
+      #####################################################################################################################
+    ...

config_files/initialization_config_2013.yml

-Original file line number
+Diff line change
@@ -0,0 +1,107 @@
+    # This YAML file is a configuration file for all
+    # initialization parameters used in Echopop
+    ---
+      #####################################################################################################################
+      # Survey data processing#
+      ########################
+      # Jolly and Hampton (1990) stratified mean calculation
+      stratified_survey_mean_parameters:
+        strata_transect_proportion: 0.75                          # percent of Jolly-Hampton transects in each stratum
+        num_replicates: 10000                                     # number of resample replicates
+        mesh_transects_per_latitude: 5                            # number of virtual transects per degree latitude in kriging mesh
+      #####################################################################################################################
+      # Biological data processing#
+      ########################
+      # Jolly and Hampton (1990) stratified mean calculation
+      bio_hake_len_bin: [                   # length sequence array 2 - 80 cm. This specifies the bin centers!
+,                    # start of bin centers
+,                   # end of bin centers
+# number of bins in total
+      ]
+      bio_hake_age_bin: [                   # age sequence array: year - age  1-22
+,                    # start of sequence
+,                   # end of sequence
+# number of points in the sequence
+      ]
+      #####################################################################################################################
+      # Acoustic transect export processing#
+      ########################
+      nasc_exports:
+        export_file_directory: /raw_nasc
+        nasc_export_directory: /Exports     # Acoustic export directory
+        save_file_template: "{REGION}_NASC_{YEAR}_table_{GROUP}.xlsx"
+        save_file_sheetname: Sheet1
+        regions:                            # Main acoustic data region names (list or single string)
+          all_ages: [Age-1 Hake,            # Age-1+
+                      Age-1 Hake Mix,
+                      Hake,
+                      Hake Mix]
+          no_age1: [Hake, Hake Mix]         # Age-2+
+        max_transect_spacing: 10.0          # Maximum transect spacing (nmi)
+        file_columns: [transect_num, region_id, distance_s, distance_e, latitude, longitude,
+                        stratum_num, transect_spacing, layer_mean_depth, layer_height, bottom_depth,
+                        NASC, haul_num]
+      transect_region_mapping:
+        parts:
+          REGION_CLASS:
+            - pattern: ^[hH](?![a-zA-Z]|1a)
+              label: Hake
+            - pattern: ^[hH]1[aA][mM]
+              label: Age-1 Hake Mix
+            - pattern: ^[hH]1[aA]
+              label: Age-1 Hake
+            - pattern: ^[hH][mM]
+              label: Hake Mix
+            - pattern: hake_mix
+              label: Hake Mix
+            - pattern: hake
+              label: Hake
+          HAUL_NUM:
+            - pattern: '[0-9]+'
+              label: None
+          COUNTRY:
+            - pattern: ^[cC]
+              label: CAN
+            - pattern: ^[uU]
+              label: US
+        pattern: "{REGION_CLASS}{HAUL_NUM}{COUNTRY}"
+        inpfc_strata_region:
+          CAN: [6]
+          US: [1, 2, 3, 4, 5]
+        save_file_template: "{COUNTRY}_{YEAR}_transect_region_haul_{GROUP}.xlsx"
+        save_file_directory: /Stratification
+        save_file_sheetname: Sheet1
+      #####################################################################################################################
+      # Log-linear regression#
+      ########################
+      # Target strength (TS) - length (L) regression: TS=m*log10(L)+b
+      TS_length_regression_parameters:
+        pacific_hake:                         # corresponding species text code
+          number_code: 22500                  # species number code
+          TS_L_slope: 20.0                    # the 'm' or 'slope' parameter
+          TS_L_intercept: -68.0               # the 'b' or 'y-intercept'
+          length_units: cm                    # units for L used in regression/relationship
+      #####################################################################################################################
+      # Geospatial settings#
+      ########################
+      geospatial:
+        init: epsg:4326                       # EPSG integer code for geodetic parameter dataset
+      #####################################################################################################################
+      # Kriging parameters#
+      #####################
+      kriging_parameters:
+        A0: 6.25                              # base area of the grid cell
+        longitude_reference: -124.78338       # longitude reference for kriging mesh adjustment
+        longitude_offset: -124.78338          # longitudinal offset for kriging mesh adjustment
+        latitude_offset: 45.0                 # latitudinal offset for kriging mesh adjustment
+      #####################################################################################################################
+    ...

config_files/initialization_config.yml → config_files/initialization_config_2015.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -42,7 +42,7 @@ @@
                       Hake Mix]
           no_age1: [Hake, Hake Mix]         # Age-2+
         max_transect_spacing: 10.0          # Maximum transect spacing (nmi)
-        file_columns: [transect_num, region_id, vessel_log_start, vessel_log_end, latitude, longitude,
+        file_columns: [transect_num, region_id, distance_s, distance_e, latitude, longitude,
                         stratum_num, transect_spacing, layer_mean_depth, layer_height, bottom_depth,
                         NASC, haul_num]
       transect_region_mapping:
@@ Expand Down @@

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