[WIP] non-local data

dacapo/apply.py

@@ -18,7 +18,7 @@
     create_weights_store,
 )
 
-from pathlib import Path
+from upath import UPath as Path
 
 logger = logging.getLogger(__name__)
 

dacapo/blockwise/argmax_worker.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 import sys
 from dacapo.experiments.datasplits.datasets.arrays.zarr_array import ZarrArray
 from dacapo.store.array_store import LocalArrayIdentifier

dacapo/blockwise/blockwise_task.py

@@ -1,6 +1,6 @@
 from datetime import datetime
 from importlib.machinery import SourceFileLoader
-from pathlib import Path
+from upath import UPath as Path
 from daisy import Task, Roi
 
 

dacapo/blockwise/predict_worker.py

@@ -1,5 +1,5 @@
 import sys
-from pathlib import Path
+from upath import UPath as Path
 from typing import Optional
 
 import torch

dacapo/blockwise/scheduler.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 import shutil
 import tempfile
 import time

dacapo/blockwise/segment_worker.py

@@ -1,7 +1,7 @@
 from importlib.machinery import SourceFileLoader
 import logging
 import os
-from pathlib import Path
+from upath import UPath as Path
 import sys
 import click
 import daisy

dacapo/blockwise/threshold_worker.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 import sys
 from dacapo.experiments.datasplits.datasets.arrays.zarr_array import ZarrArray
 from dacapo.store.array_store import LocalArrayIdentifier

dacapo/cli.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 from typing import Optional
 
 import numpy as np

dacapo/compute_context/bsub.py

@@ -1,5 +1,5 @@
 import os
-from pathlib import Path
+from upath import UPath as Path
 from .compute_context import ComputeContext
 import daisy
 

dacapo/experiments/datasplits/datasets/arrays/tiff_array.py

@@ -6,7 +6,7 @@
 import tifffile
 
 import logging
-from pathlib import Path
+from upath import UPath as Path
 from typing import List, Optional
 
 logger = logging.getLogger(__name__)

dacapo/experiments/datasplits/datasets/arrays/tiff_array_config.py

@@ -5,7 +5,7 @@
 
 from funlib.geometry import Coordinate
 
-from pathlib import Path
+from upath import UPath as Path
 from typing import List
 
 

dacapo/experiments/datasplits/datasets/arrays/zarr_array.py

@@ -12,7 +12,7 @@
 
 from collections import OrderedDict
 import logging
-from pathlib import Path
+from upath import UPath as Path
 import json
 from typing import Dict, Tuple, Any, Optional, List
 

dacapo/experiments/datasplits/datasets/arrays/zarr_array_config.py

@@ -5,7 +5,7 @@
 
 from funlib.geometry import Coordinate
 
-from pathlib import Path
+from upath import UPath as Path
 
 from typing import Optional, List, Tuple
 

dacapo/experiments/tasks/post_processors/argmax_post_processor.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 from dacapo.blockwise import run_blockwise
 import dacapo.blockwise
 from dacapo.experiments.datasplits.datasets.arrays.zarr_array import ZarrArray

dacapo/experiments/tasks/post_processors/threshold_post_processor.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 from dacapo.blockwise.scheduler import run_blockwise
 from dacapo.experiments.datasplits.datasets.arrays.zarr_array import ZarrArray
 from .threshold_post_processor_parameters import ThresholdPostProcessorParameters

dacapo/experiments/tasks/post_processors/watershed_post_processor.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 import dacapo.blockwise
 from dacapo.blockwise.scheduler import segment_blockwise
 from dacapo.experiments.datasplits.datasets.arrays import ZarrArray

dacapo/experiments/tasks/pretrained_task_config.py

@@ -3,7 +3,7 @@
 from .pretrained_task import PretrainedTask
 from .task_config import TaskConfig
 
-from pathlib import Path
+from upath import UPath as Path
 
 
 @attr.s

dacapo/options.py

@@ -2,7 +2,7 @@
 import yaml
 import logging
 from os.path import expanduser
-from pathlib import Path
+from upath import UPath as Path
 
 import attr
 from cattr import Converter

dacapo/predict.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+from upath import UPath as Path
 
 from dacapo.blockwise import run_blockwise
 import dacapo.blockwise

dacapo/store/array_store.py

@@ -7,7 +7,7 @@
 from abc import ABC, abstractmethod
 import itertools
 import json
-from pathlib import Path
+from upath import UPath as Path
 from typing import Optional, Tuple
 
 

dacapo/store/conversion_hooks.py

@@ -14,7 +14,7 @@
 
 from funlib.geometry import Coordinate, Roi
 
-from pathlib import Path
+from upath import UPath as Path
 
 
 def register_hierarchy_hooks(converter):

dacapo/store/create_store.py

@@ -6,7 +6,7 @@
 from .file_stats_store import FileStatsStore
 from dacapo import Options
 
-from pathlib import Path
+from upath import UPath as Path
 
 
 def create_config_store():

dacapo/store/file_config_store.py

@@ -9,7 +9,7 @@
 
 import logging
 import yaml
-from pathlib import Path
+from upath import UPath as Path
 
 logger = logging.getLogger(__name__)
 

dacapo/store/file_stats_store.py

@@ -6,7 +6,7 @@
 
 import logging
 import pickle
-from pathlib import Path
+from upath import UPath as Path
 
 logger = logging.getLogger(__name__)
 

dacapo/store/local_array_store.py

@@ -1,6 +1,6 @@
 from .array_store import ArrayStore, LocalArrayIdentifier, LocalContainerIdentifier
 
-from pathlib import Path
+from upath import UPath as Path
 import logging
 import shutil
 from typing import Optional, Tuple

dacapo/store/local_weights_store.py

@@ -5,7 +5,7 @@
 import torch
 
 import json
-from pathlib import Path
+from upath import UPath as Path
 import logging
 from typing import Optional, Union
 

dacapo/validate.py

@@ -8,7 +8,7 @@
     create_weights_store,
 )
 
-from pathlib import Path
+from upath import UPath as Path
 import logging
 from warnings import warn
 

pyproject.toml

@@ -27,6 +27,7 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
+        "universal-pathlib>=0.2.2,<1.0.0",
         "numpy>=1.22.4",
         "pyyaml",
         "zarr",