updating code for pydantic v2 (#160)

* updating code for pydantic v2 * update for iohub in stable version * update TransformationMeta import from iohub.ngff_meta to iohub.ngff * update channel_display_settings import from iohub.display_utils to iohub.ngff * update channel_display_settings import from iohub.ngff to iohub.ngff.disply and sorting imports for style correction * imports organization for style test * imports organization for style test * imports organization for style test --------- Co-authored-by: Taylla Milena Theodoro <[email protected]>
czbiohub-sf · Sep 19, 2024 · 9727c79 · 9727c79
1 parent 8f2469b
commit 9727c79
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Showing 11 changed files with 16 additions and 16 deletions.
diff --git a/mantis/acquisition/AcquisitionSettings.py b/mantis/acquisition/AcquisitionSettings.py
@@ -5,8 +5,8 @@
 
 import numpy as np
 
-from pydantic import ConfigDict, NonNegativeFloat, NonNegativeInt, validator
-from pydantic.dataclasses import dataclass
+from pydantic.v1 import ConfigDict, NonNegativeFloat, NonNegativeInt, validator
+from pydantic.v1.dataclasses import dataclass
 
 config = ConfigDict(extra='forbid')
 

diff --git a/mantis/acquisition/scripts/measure_psf.py b/mantis/acquisition/scripts/measure_psf.py
@@ -7,7 +7,7 @@
 import numpy as np
 import torch
 
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import TransformationMeta
 from iohub.reader import open_ome_zarr
 from pycromanager import Acquisition, Core, multi_d_acquisition_events
 

diff --git a/mantis/analysis/AnalysisSettings.py b/mantis/analysis/AnalysisSettings.py
@@ -5,7 +5,7 @@
 import numpy as np
 import torch
 
-from pydantic import BaseModel, Extra, NonNegativeInt, PositiveFloat, PositiveInt, validator
+from pydantic.v1 import BaseModel, Extra, NonNegativeInt, PositiveFloat, PositiveInt, validator
 
 
 # All settings classes inherit from MyBaseModel, which forbids extra parameters to guard against typos

diff --git a/mantis/analysis/scripts/simple_phase_recon.py b/mantis/analysis/scripts/simple_phase_recon.py
@@ -4,7 +4,7 @@
 import numpy as np
 
 from iohub import open_ome_zarr, read_micromanager
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import TransformationMeta
 from recOrder.compute.reconstructions import initialize_reconstructor, reconstruct_phase3D
 
 # %% Load data

diff --git a/mantis/cli/estimate_bleaching.py b/mantis/cli/estimate_bleaching.py
@@ -8,8 +8,8 @@
 import matplotlib.pyplot as plt
 import numpy as np
 
-from iohub.display_utils import channel_display_settings
-from iohub.ngff import open_ome_zarr
+from iohub import open_ome_zarr
+from iohub.ngff.display import channel_display_settings
 from scipy.optimize import curve_fit
 from tqdm import tqdm
 

diff --git a/mantis/cli/estimate_psf.py b/mantis/cli/estimate_psf.py
@@ -8,8 +8,8 @@
 import numpy as np
 import torch
 
-from iohub.ngff import open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub import open_ome_zarr
+from iohub.ngff import TransformationMeta
 
 from mantis.analysis.AnalysisSettings import PsfFromBeadsSettings
 from mantis.analysis.analyze_psf import detect_peaks, extract_beads

diff --git a/mantis/cli/stitch.py b/mantis/cli/stitch.py
@@ -9,7 +9,7 @@
 import pandas as pd
 
 from iohub import open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import TransformationMeta
 from slurmkit import HAS_SLURM, SlurmParams, slurm_function, submit_function
 
 from mantis.analysis.AnalysisSettings import StitchSettings

diff --git a/mantis/cli/update_scale_metadata.py b/mantis/cli/update_scale_metadata.py
@@ -3,7 +3,7 @@
 import click
 
 from iohub import open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub.ngff import TransformationMeta
 
 from mantis.cli.parsing import input_position_dirpaths
 

diff --git a/mantis/cli/utils.py b/mantis/cli/utils.py
@@ -12,8 +12,8 @@
 import numpy as np
 import yaml
 
-from iohub.ngff import Position, open_ome_zarr
-from iohub.ngff_meta import TransformationMeta
+from iohub import open_ome_zarr
+from iohub.ngff import Position, TransformationMeta
 from numpy.typing import DTypeLike
 from tqdm import tqdm
 

diff --git a/mantis/tests/test_analysis/test_analysis_settings.py b/mantis/tests/test_analysis/test_analysis_settings.py
@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 from mantis.analysis.AnalysisSettings import (
     DeskewSettings,

diff --git a/pyproject.toml b/pyproject.toml
@@ -21,7 +21,7 @@ classifiers = [
 # list package dependencies here
 dependencies = [
   "copylot @ git+https://github.com/czbiohub-sf/coPylot",
-  "iohub==0.1.0",
+  "iohub==0.2.0a1",
   "matplotlib",
   "napari; 'arm64' in platform_machine",                 # without Qt5 and skimage
   "napari[all]; 'arm64' not in platform_machine",        # with Qt5 and skimage
@@ -34,7 +34,7 @@ dependencies = [
   "monai",
   "pandas~=2.1",
   "pycromanager==0.28.1",
-  "pydantic",
+  "pydantic>=2.0.0",
   "pylablib==1.4.1",
   "scipy",
   "slurmkit @ git+https://github.com/royerlab/slurmkit",