water-column-sonar-processing 0.0.4__py3-none-any.whl → 0.0.5__py3-none-any.whl

{aws_manager → water_column_sonar_processing/aws}/dynamodb_manager.py

@@ -23,7 +23,7 @@ class DynamoDBManager:
         self.type_deserializer = TypeDeserializer()
 
     #####################################################################
-    ### defined in raw-to-zarr_manager, not used
+    ### defined in raw-to-model, not used
     # def put_item(
     #         self,
     #         table_name,

{aws_manager → water_column_sonar_processing/aws}/s3_manager.py

@@ -139,12 +139,12 @@ class S3Manager:
         return all_uploads
 
     #####################################################################
-    def upload_zarr_files_to_bucket(  # noaa-wcsd-zarr_manager-pds
+    def upload_zarr_files_to_bucket(  # noaa-wcsd-model-pds
             self,
             local_directory,
             remote_directory,
     ):
-        # Right now this is just for uploading a zarr_manager store to s3
+        # Right now this is just for uploading a model store to s3
         print('Uploading files to output bucket.')
         store_name = os.path.basename(local_directory)
         all_files = []
@@ -162,8 +162,8 @@ class S3Manager:
         return all_uploads
 
     #####################################################################
-    # used: raw-to-zarr_manager
-    def list_objects(  # noaa-wcsd-pds and noaa-wcsd-zarr_manager-pds
+    # used: raw-to-model
+    def list_objects(  # noaa-wcsd-pds and noaa-wcsd-model-pds
             self,
             bucket_name,
             prefix
@@ -179,7 +179,7 @@ class S3Manager:
                 keys.extend([k['Key'] for k in page['Contents']])
         return keys
 
-    def list_nodd_objects(  # These are used by the geometry_manager for uploading data
+    def list_nodd_objects(  # These are used by the geometry for uploading data
             self,
             prefix,
     ):
@@ -250,8 +250,8 @@ class S3Manager:
         return raw_files
 
     #####################################################################
-    def get_object(  # TODO: Move this to index_manager.py
-                     # noaa-wcsd-pds or noaa-wcsd-zarr_manager-pds
+    def get_object(  # TODO: Move this to index.py
+                     # noaa-wcsd-pds or noaa-wcsd-model-pds
             self,
             bucket_name,
             key_name,
@@ -272,9 +272,9 @@ class S3Manager:
         return response
 
     #####################################################################
-    # used raw-to-zarr_manager
+    # used raw-to-model
     def download_file(  # TODO: change to download_object
-                        # noaa-wcsd-pds or noaa-wcsd-zarr_manager-pds
+                        # noaa-wcsd-pds or noaa-wcsd-model-pds
             self,
             bucket_name,
             key,
@@ -289,7 +289,7 @@ class S3Manager:
 
     #####################################################################
     # not used
-    # def delete_nodd_object(  # noaa-wcsd-zarr_manager-pds
+    # def delete_nodd_object(  # noaa-wcsd-model-pds
     #         self,
     #         bucket_name,
     #         key
@@ -319,7 +319,7 @@ class S3Manager:
 
     #####################################################################
     # not used TODO: remove
-    def put(  # noaa-wcsd-zarr_manager-pds
+    def put(  # noaa-wcsd-model-pds
             self,
             bucket_name,
             key,

{cruise → water_column_sonar_processing/cruise}/create_empty_zarr_store.py

@@ -2,17 +2,17 @@ import os
 import numcodecs
 import numpy as np
 
-from utility.cleaner import Cleaner
-from aws_manager.dynamodb_manager import DynamoDBManager
-from aws_manager.s3_manager import S3Manager
-from zarr_manager.zarr_manager import ZarrManager
+from water_column_sonar_processing.utility.cleaner import Cleaner
+from water_column_sonar_processing.aws.dynamodb_manager import DynamoDBManager
+from water_column_sonar_processing.aws.s3_manager import S3Manager
+from water_column_sonar_processing.model.zarr_manager import ZarrManager
 
 numcodecs.blosc.use_threads = False
 numcodecs.blosc.set_nthreads(1)
 
 TEMPDIR = "/tmp"
 
-# TODO: when ready switch to version 3 of zarr_manager spec
+# TODO: when ready switch to version 3 of model spec
 # ZARR_V3_EXPERIMENTAL_API = 1
 # creates the latlon data: foo = ep.consolidate.add_location(ds_Sv, echodata)
 
@@ -34,7 +34,7 @@ class CreateEmptyZarrStore:
             object_prefix: str,
             cruise_name: str,
     ) -> None:
-        print('uploading zarr_manager store to s3')
+        print('uploading model store to s3')
         s3_manager = S3Manager()
         #
         print('Starting upload with thread pool executor.')
@@ -43,8 +43,8 @@ class CreateEmptyZarrStore:
         for subdir, dirs, files in os.walk(f"{local_directory}/{cruise_name}.zarr_manager"):
             for file in files:
                 local_path = os.path.join(subdir, file)
-                # 'level_2/Henry_B._Bigelow/HB0806/EK60/HB0806.zarr_manager/.zattrs'
-                s3_key = f'{object_prefix}/{cruise_name}.zarr_manager{local_path.split(f"{cruise_name}.zarr_manager")[-1]}'
+                # 'level_2/Henry_B._Bigelow/HB0806/EK60/HB0806.model/.zattrs'
+                s3_key = f'{object_prefix}/{cruise_name}.model{local_path.split(f"{cruise_name}.model")[-1]}'
                 all_files.append([local_path, s3_key])
         #
         # print(all_files)
@@ -98,10 +98,10 @@ class CreateEmptyZarrStore:
             new_width = int(consolidated_zarr_width)
             print(f"new_width: {new_width}")
             #################################################################
-            store_name = f"{cruise_name}.zarr_manager"
+            store_name = f"{cruise_name}.model"
             print(store_name)
             ################################################################
-            # Delete existing zarr_manager store if it exists
+            # Delete existing model store if it exists
             s3_manager = S3Manager()
             zarr_prefix = os.path.join("level_2", ship_name, cruise_name, sensor_name)
             child_objects = s3_manager.get_child_objects(
@@ -113,7 +113,7 @@ class CreateEmptyZarrStore:
                     objects=child_objects,
                 )
             ################################################################
-            # Create new zarr_manager store
+            # Create new model store
             zarr_manager = ZarrManager()
             new_height = len(zarr_manager.get_depth_values(
                 min_echo_range=cruise_min_echo_range,
@@ -157,11 +157,11 @@ class CreateEmptyZarrStore:
             # TODO: update enum in dynamodb
             #################################################################
         except Exception as err:
-            print(f"Problem trying to create new cruise zarr_manager store: {err}")
+            print(f"Problem trying to create new cruise model store: {err}")
         finally:
             cleaner = Cleaner()
             cleaner.delete_local_files()
-        print("Done creating cruise level zarr_manager store")
+        print("Done creating cruise level model store")
 
 
 ###########################################################

{cruise → water_column_sonar_processing/cruise}/resample_regrid.py

@@ -6,16 +6,16 @@ import numpy as np
 import xarray as xr
 import pandas as pd
 
-from aws_manager.dynamodb_manager import DynamoDBManager
-from zarr_manager.zarr_manager import ZarrManager
-from geometry_manager.geometry_manager import GeometryManager
+from water_column_sonar_processing.aws.dynamodb_manager import DynamoDBManager
+from water_column_sonar_processing.model.zarr_manager import ZarrManager
+from water_column_sonar_processing.geometry.geometry_manager import GeometryManager
 
 
 numcodecs.blosc.use_threads = False
 numcodecs.blosc.set_nthreads(1)
 
 
-# TODO: when ready switch to version 3 of zarr_manager spec
+# TODO: when ready switch to version 3 of model spec
 #  ZARR_V3_EXPERIMENTAL_API = 1
 #  creates the latlon data: foo = ep.consolidate.add_location(ds_Sv, echodata)
 
@@ -115,7 +115,7 @@ class ResampleRegrid:
     ) -> None:
         """
         The goal here is to interpolate the data against the depth values already populated
-        in the existing file level zarr_manager stores. We open the cruise-level store with zarr_manager for
+        in the existing file level model stores. We open the cruise-level store with model for
         read/write operations. We open the file-level store with Xarray to leverage tools for
         resampling and subsetting the data.
         """
@@ -124,7 +124,7 @@ class ResampleRegrid:
             zarr_manager = ZarrManager()
             # s3_manager = S3Manager()
             geo_manager = GeometryManager()
-            # get zarr_manager store
+            # get model store
             output_zarr_store = zarr_manager.open_s3_zarr_store_with_zarr(
                 ship_name=ship_name,
                 cruise_name=cruise_name,
@@ -157,7 +157,7 @@ class ResampleRegrid:
                 # TODO: filter rows by enum success, filter the dataframe just for enums >= LEVEL_1_PROCESSING
                 #  df[df['PIPELINE_STATUS'] < PipelineStatus.LEVEL_1_PROCESSING] = np.nan
 
-                # Get index_manager from all cruise files. Note: should be based on which are included in cruise.
+                # Get index from all cruise files. Note: should be based on which are included in cruise.
                 index = cruise_df.index[cruise_df['FILE_NAME'] == f"{file_name_stem}.raw"][0]
 
                 # get input store
@@ -169,7 +169,7 @@ class ResampleRegrid:
                 )
                 #########################################################################
                 # [3] Get needed indices
-                # Offset from start index_manager to insert new data. Note that missing values are excluded.
+                # Offset from start index to insert new data. Note that missing values are excluded.
                 ping_time_cumsum = np.insert(
                     np.cumsum(cruise_df['NUM_PING_TIME_DROPNA'].dropna().to_numpy(dtype=int)),
                     obj=0,
@@ -223,7 +223,7 @@ class ResampleRegrid:
                 print(f"start_ping_time_index: {start_ping_time_index}, end_ping_time_index: {end_ping_time_index}")
 
                 #########################################################################
-                # write Sv values to cruise-level-zarr_manager-store
+                # write Sv values to cruise-level-model-store
                 for channel in range(len(input_xr.channel.values)):  # doesn't like being written in one fell swoop :(
                     output_zarr_store.Sv[
                         :,

{geometry_manager → water_column_sonar_processing/geometry}/geometry_manager.py

@@ -3,8 +3,8 @@ import numpy as np
 import geopandas
 import pandas as pd
 
-from utility.cleaner import Cleaner
-from aws_manager.s3_manager import S3Manager
+from water_column_sonar_processing.utility.cleaner import Cleaner
+from water_column_sonar_processing.aws.s3_manager import S3Manager
 
 """
 //  [Decimal / Places / Degrees	/ Object that can be recognized at scale / N/S or E/W at equator, E/W at 23N/S, E/W at 45N/S, E/W at 67N/S]

{geometry_manager → water_column_sonar_processing/geometry}/pmtile_generation.py

@@ -23,7 +23,7 @@ class PMTileGeneration(object):
 
     #######################################################
     def generate_geojson_feature_collection(self):
-        # This was used to read from noaa-wcsd-zarr_manager-pds bucket geojson files and then to
+        # This was used to read from noaa-wcsd-model-pds bucket geojson files and then to
         # generate the geopandas dataframe which could be exported to another comprehensive
         # geojson file. That
         result = list(Path("/Users/r2d2/Documents/echofish/geojson").rglob("*.json"))

{index_manager → water_column_sonar_processing/index}/index_manager.py

@@ -4,7 +4,7 @@ import pandas as pd
 from datetime import datetime
 from concurrent.futures import ThreadPoolExecutor
 from concurrent.futures import as_completed
-from aws_manager.s3_manager import S3Manager
+from water_column_sonar_processing.aws.s3_manager import S3Manager
 
 class IndexManager:
 
@@ -193,7 +193,7 @@ class IndexManager:
         return calibration_statuses
 
     #################################################################
-    # def index_manager(  # TODO: get rid of this?
+    # def index(  # TODO: get rid of this?
     #         self
     # ):
     #     start_time = datetime.now()  # used for benchmarking

{zarr_manager → water_column_sonar_processing/model}/zarr_manager.py

@@ -4,20 +4,18 @@ import numcodecs
 import numpy as np
 import xarray as xr
 from numcodecs import Blosc
-
-from utility.constants import Constants, Coordinates
-from utility.timestamp import Timestamp
-from aws_manager.s3fs_manager import S3FSManager
+from water_column_sonar_processing.utility.constants import Constants, Coordinates
+from water_column_sonar_processing.utility.timestamp import Timestamp
+from water_column_sonar_processing.aws.s3fs_manager import S3FSManager
 
 numcodecs.blosc.use_threads = False
 numcodecs.blosc.set_nthreads(1)
 
 
-# TODO: when ready switch to version 3 of zarr_manager spec
+# TODO: when ready switch to version 3 of model spec
 # ZARR_V3_EXPERIMENTAL_API = 1
 
 # creates the latlon data: foo = ep.consolidate.add_location(ds_Sv, echodata)
-
 class ZarrManager:
     #######################################################
     def __init__(
@@ -37,7 +35,7 @@ class ZarrManager:
             max_echo_range: float = 100.,  # maximum depth measured from whole cruise
     ):
         # Gets the set of depth values that will be used when resampling and
-        # regridding the data to a cruise level zarr_manager store.
+        # regridding the data to a cruise level model store.
         # Note: returned values do not start at zero.
         print('Getting depth values.')
         all_cruise_depth_values = np.linspace(
@@ -252,7 +250,7 @@ class ZarrManager:
             s3fs_manager = S3FSManager()
             root = f'{self.output_bucket_name}/level_2/{ship_name}/{cruise_name}/{sensor_name}/{cruise_name}.zarr'
             store = s3fs_manager.s3_map(s3_zarr_store_path=root)
-            # synchronizer = zarr_manager.ProcessSynchronizer(f"/tmp/{ship_name}_{cruise_name}.sync")
+            # synchronizer = model.ProcessSynchronizer(f"/tmp/{ship_name}_{cruise_name}.sync")
             cruise_zarr = zarr.open(store=store, mode="r+")
         except Exception as err:  # Failure
             print(f'Exception encountered opening Zarr store with Zarr.: {err}')
@@ -284,12 +282,12 @@ class ZarrManager:
 
     #######################################################
     # def create_process_synchronizer(self):
-    #     # TODO: explore aws_manager redis options
+    #     # TODO: explore aws redis options
     #     pass
 
     #######################################################
     # def verify_cruise_store_data(self):
-    #     # TODO: run a check on a finished zarr_manager store to ensure that
+    #     # TODO: run a check on a finished model store to ensure that
     #     #   none of the time, latitude, longitude, or depth values
     #     #   are NaN.
     #     pass

model.py → water_column_sonar_processing/process.py

@@ -1,13 +1,13 @@
 import os
 import json
 import numpy as np
-from aws_manager.s3_manager import S3Manager
-from aws_manager.s3fs_manager import S3FSManager
-from aws_manager.sns_manager import SNSManager
-from aws_manager.dynamodb_manager import DynamoDBManager
+from water_column_sonar_processing.aws.s3_manager import S3Manager
+from water_column_sonar_processing.aws.s3fs_manager import S3FSManager
+from water_column_sonar_processing.aws.sns_manager import SNSManager
+from water_column_sonar_processing.aws.dynamodb_manager import DynamoDBManager
 
 ###########################################################
-class Model:
+class Process:
     #######################################################
     def __init__(
             self,
@@ -87,7 +87,7 @@ class Model:
                 ':sh': {'S': ship_name},
                 ':st': {'S': '2006-04-06T11:34:07.288Z'},
                 ':zb': {'S': 'r2d2-dev-echofish2-118234403147-echofish-dev-output'},
-                ':zp': {'S': 'level_1/David_Starr_Jordan/DS0604/EK60/DSJ0604-D20060406-T113407.zarr_manager'},
+                ':zp': {'S': 'level_1/David_Starr_Jordan/DS0604/EK60/DSJ0604-D20060406-T113407.model'},
             },
             update_expression=(
                 'SET '

{utility → water_column_sonar_processing/utility}/cleaner.py

@@ -7,9 +7,9 @@ import shutil
 class Cleaner:
     @staticmethod
     def delete_local_files(
-            file_types=['*.raw*', '*.zarr_manager']  # '*.json'
+            file_types=['*.raw*', '*.model']  # '*.json'
     ):
-        print('Deleting all local raw and zarr_manager files')
+        print('Deleting all local raw and model files')
         for i in file_types:
             for j in glob.glob(i):
                 if os.path.isdir(j):

{water_column_sonar_processing-0.0.4.dist-info → water_column_sonar_processing-0.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: water_column_sonar_processing
-Version: 0.0.4
+Version: 0.0.5
 Summary: A processing tool for water column sonar data.
 Author-email: Rudy Klucik <rudy.klucik@noaa.gov>
 Project-URL: Homepage, https://github.com/CI-CMG/water-column-sonar-processing

water_column_sonar_processing-0.0.5.dist-info/RECORD

@@ -0,0 +1,29 @@
+water_column_sonar_processing/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+water_column_sonar_processing/process.py,sha256=Wu3hcSbsB52gM8bAELKd0n206tdOTfzd3LDpFVCzhYg,5337
+water_column_sonar_processing/aws/__init__.py,sha256=pYvL00VjrwCe9k5jfof2k-nc9IG1N-hy1k95W7VlKOs,162
+water_column_sonar_processing/aws/dynamodb_manager.py,sha256=Z1-fhr2X6B_wIlIHMYPTgvwkhccYn75U2XZYNP2pJvI,5339
+water_column_sonar_processing/aws/s3_manager.py,sha256=IJb8hlMGZr5COs2CbOEZvJvRZHw3UN6cNft20soyqbw,13402
+water_column_sonar_processing/aws/s3fs_manager.py,sha256=k4nW48E0reQwj1t4pe_ybK5kX0H1SHeG8urddHelGZ4,2463
+water_column_sonar_processing/aws/sns_manager.py,sha256=IR5Y3MvwYFjd-eSg4tEjoNyABGxdJb85wOj0I-vckX0,2204
+water_column_sonar_processing/aws/sqs_manager.py,sha256=VQSkxYtdhH4zfZqQl5FiNE2_svczN0hU-UBgbviwvtc,1696
+water_column_sonar_processing/cruise/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+water_column_sonar_processing/cruise/create_empty_zarr_store.py,sha256=dkJzNZmD51TSphhWVq9qbO32L54ipXREYwT7DYCek_8,7039
+water_column_sonar_processing/cruise/resample_regrid.py,sha256=-YFSKljnuKqn8PkhmfhDwrQHuvziApJWwS-zU3l0ZO4,11327
+water_column_sonar_processing/geometry/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+water_column_sonar_processing/geometry/geometry_manager.py,sha256=d6uKXsxcVfoDpVqr92YyRemLL9g-VDxCttjadPAKt34,9461
+water_column_sonar_processing/geometry/geometry_simplification.py,sha256=_TCrlxqWlhO05Od3ZB4Sfgob9p3tQr3r1vjseG0qMNQ,3071
+water_column_sonar_processing/geometry/pmtile_generation.py,sha256=sXKFKmSu33bOdPBmW5FHpMsKLf6SFlgv7QznqsJ_Ko4,2791
+water_column_sonar_processing/index/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+water_column_sonar_processing/index/index_manager.py,sha256=novA5ZutVkSU_miC1IYG1OCjUkxLBlbij68o87eCQz0,10732
+water_column_sonar_processing/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+water_column_sonar_processing/model/zarr_manager.py,sha256=zNbrQAtNoszenfoJ6Y9TJzkcAAKJKEf4DXKMHAIdv_c,12452
+water_column_sonar_processing/utility/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+water_column_sonar_processing/utility/cleaner.py,sha256=oa6pt--HVrlCx6rSWkTbCQBSAlFushrOPzW4JT5fzTc,601
+water_column_sonar_processing/utility/constants.py,sha256=uTuSyH9YGG8bDd5xNbT4zA5O_lu874C-8m1MRvVppPw,1631
+water_column_sonar_processing/utility/pipeline_status.py,sha256=iRLyzI3gsesyz0I4NukbJwqiRmXgSZBOdB3C1x2eMSg,4185
+water_column_sonar_processing/utility/timestamp.py,sha256=i4ub7ob24edHU2yt4aOmvle_Nmlf1F_9HVGa9TJ5HgM,359
+water_column_sonar_processing-0.0.5.dist-info/LICENSE,sha256=lz4IpJ5_adG3S0ali-WaIpQFVTnEAOucMDQPECUVEYw,1110
+water_column_sonar_processing-0.0.5.dist-info/METADATA,sha256=gQwpPMJaL4v90Nk34OFi1XMM_LX3Yj320JKSYghjDWU,3157
+water_column_sonar_processing-0.0.5.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+water_column_sonar_processing-0.0.5.dist-info/top_level.txt,sha256=aRYU4A7RNBlNrL4vzjytFAir3BNnmOgsvIGKKA36tg4,30
+water_column_sonar_processing-0.0.5.dist-info/RECORD,,

water_column_sonar_processing-0.0.5.dist-info/top_level.txt

@@ -0,0 +1 @@
+water_column_sonar_processing

water_column_sonar_processing-0.0.4.dist-info/RECORD

@@ -1,29 +0,0 @@
-__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-model.py,sha256=r5S-ZZEV1lJdpEU7yzGKD9WIWuRRjaw1d7gdGQoBaTo,5254
-aws_manager/__init__.py,sha256=pYvL00VjrwCe9k5jfof2k-nc9IG1N-hy1k95W7VlKOs,162
-aws_manager/dynamodb_manager.py,sha256=dy2IUqQMlyXbnSGgJWt4ggxUnu2heb_Z2jgueaUkCzQ,5346
-aws_manager/s3_manager.py,sha256=r5CJ0XIvA_i4azFvLF4xKdcCuhKBJRNFOL2luvpIBnM,13481
-aws_manager/s3fs_manager.py,sha256=k4nW48E0reQwj1t4pe_ybK5kX0H1SHeG8urddHelGZ4,2463
-aws_manager/sns_manager.py,sha256=IR5Y3MvwYFjd-eSg4tEjoNyABGxdJb85wOj0I-vckX0,2204
-aws_manager/sqs_manager.py,sha256=VQSkxYtdhH4zfZqQl5FiNE2_svczN0hU-UBgbviwvtc,1696
-cruise/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cruise/create_empty_zarr_store.py,sha256=K_Jfm_7Rt8snBXLQOJOjYilPH3pUXHveql9hay8HvCE,7012
-cruise/resample_regrid.py,sha256=Do6j-OhU8t4n10EkHRSyPC5MfqbAwA829q9S_cd4W1U,11311
-geometry_manager/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geometry_manager/geometry_manager.py,sha256=tCNatSleMCJhGxLp9H_WYr1MquBU9sBCFWsZ1o0rTL4,9409
-geometry_manager/geometry_simplification.py,sha256=_TCrlxqWlhO05Od3ZB4Sfgob9p3tQr3r1vjseG0qMNQ,3071
-geometry_manager/pmtile_generation.py,sha256=7v1XZKprlNV_fFWXHWD6mn4z0xf21rpUMqj3RLIAgy8,2798
-index_manager/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-water_column_sonar_processing-0.0.4.dist-info/RECORD,,

water_column_sonar_processing-0.0.4.dist-info/top_level.txt

@@ -1,8 +0,0 @@
-__init__
-aws_manager
-cruise
-geometry_manager
-index_manager
-model
-utility
-zarr_manager