Merge pull request #765 from fractal-analytics-platform/pydantic_v2

Relax pydantic requirements || Switch to transitional pydantic.v1

Author: lorenzocerrone

CHANGELOG.md

@@ -8,6 +8,7 @@
     * Refactor Cellpose Task inputs: Support independent normalization of 2 input channels in the Cellpose task (\#738).
     * Rename `task.cellpose_transforms` into `tasks.cellpose_utils` (\#738).
 * Development:
+    * Switch to transitional pydantic.v1 imports, changes pydantic requirement to `==1.10.16` or `>=2.6.3` (\#760).
     * Support JSON-Schema generation for `Enum` task arguments (\#749).
     * Make JSON-Schema generation tools more flexible, to simplify testing (\#749).
 * Update documentation (\#751).

fractal_tasks_core/__init__.py

@@ -1,6 +1,26 @@
 import logging
 
 
+def _check_pydantic_version():
+    """
+    Temporary check for pydantic version.
+    To be removed after moving to pydantic v2 is complete.
+    """
+    import importlib.metadata
+    from packaging import version
+
+    pydantic_version = version.parse(importlib.metadata.version("pydantic"))
+    pydantic_v1 = version.parse("1.10.16")
+    pydantic_v2 = version.parse("2.6.3")
+    if pydantic_version != pydantic_v1 and pydantic_version < pydantic_v2:
+        raise ImportError(
+            f"Pydantic version {pydantic_version} is not supported. "
+            f"Please use version =={pydantic_v1} or  >={pydantic_v2}."
+        )
+
+
+_check_pydantic_version()
+
 logging.basicConfig(
     level=logging.INFO, format="%(asctime)s; %(levelname)s; %(message)s"
 )

fractal_tasks_core/channels.py

@@ -18,8 +18,8 @@
 from typing import Union
 
 import zarr
-from pydantic import BaseModel
-from pydantic import validator
+from pydantic.v1 import BaseModel
+from pydantic.v1 import validator
 
 from fractal_tasks_core import __OME_NGFF_VERSION__
 

fractal_tasks_core/dev/lib_args_schemas.py

@@ -21,11 +21,11 @@
 from typing import Optional
 
 from docstring_parser import parse as docparse
-from pydantic.decorator import ALT_V_ARGS
-from pydantic.decorator import ALT_V_KWARGS
-from pydantic.decorator import V_DUPLICATE_KWARGS
-from pydantic.decorator import V_POSITIONAL_ONLY_NAME
-from pydantic.decorator import ValidatedFunction
+from pydantic.v1.decorator import ALT_V_ARGS
+from pydantic.v1.decorator import ALT_V_KWARGS
+from pydantic.v1.decorator import V_DUPLICATE_KWARGS
+from pydantic.v1.decorator import V_POSITIONAL_ONLY_NAME
+from pydantic.v1.decorator import ValidatedFunction
 
 from fractal_tasks_core.dev.lib_descriptions import (
     _get_class_attrs_descriptions,

fractal_tasks_core/dev/lib_signature_constraints.py

@@ -15,10 +15,10 @@
 from pathlib import Path
 from typing import Callable
 
-from pydantic.decorator import ALT_V_ARGS
-from pydantic.decorator import ALT_V_KWARGS
-from pydantic.decorator import V_DUPLICATE_KWARGS
-from pydantic.decorator import V_POSITIONAL_ONLY_NAME
+from pydantic.v1.decorator import ALT_V_ARGS
+from pydantic.v1.decorator import ALT_V_KWARGS
+from pydantic.v1.decorator import V_DUPLICATE_KWARGS
+from pydantic.v1.decorator import V_POSITIONAL_ONLY_NAME
 
 FORBIDDEN_PARAM_NAMES = (
     "args",

fractal_tasks_core/dev/task_models.py

@@ -18,7 +18,7 @@
 from typing import Any
 from typing import Optional
 
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel
 
 
 class _BaseTask(BaseModel):

fractal_tasks_core/labels.py

@@ -16,7 +16,7 @@
 from typing import Optional
 
 import zarr.hierarchy
-from pydantic.error_wrappers import ValidationError
+from pydantic.v1.error_wrappers import ValidationError
 
 from fractal_tasks_core.ngff import NgffImageMeta
 from fractal_tasks_core.zarr_utils import OverwriteNotAllowedError

fractal_tasks_core/ngff/specs.py

@@ -7,9 +7,9 @@
 from typing import Optional
 from typing import Union
 
-from pydantic import BaseModel
-from pydantic import Field
-from pydantic import validator
+from pydantic.v1 import BaseModel
+from pydantic.v1 import Field
+from pydantic.v1 import validator
 
 
 logger = logging.getLogger(__name__)

fractal_tasks_core/roi/v1_checks.py

@@ -17,7 +17,7 @@
 
 import anndata as ad
 import zarr
-from pydantic.error_wrappers import ValidationError
+from pydantic.v1.error_wrappers import ValidationError
 
 from fractal_tasks_core.tables.v1 import MaskingROITableAttrs
 

fractal_tasks_core/tables/v1.py

@@ -11,9 +11,9 @@
 import anndata as ad
 import zarr.hierarchy
 from anndata.experimental import write_elem
-from pydantic import BaseModel
-from pydantic import validator
-from pydantic.error_wrappers import ValidationError
+from pydantic.v1 import BaseModel
+from pydantic.v1 import validator
+from pydantic.v1.error_wrappers import ValidationError
 
 from fractal_tasks_core.zarr_utils import OverwriteNotAllowedError
 

fractal_tasks_core/tasks/apply_registration_to_image.py

@@ -21,7 +21,7 @@
 import dask.array as da
 import numpy as np
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 from fractal_tasks_core.ngff import load_NgffImageMeta
 from fractal_tasks_core.ngff.zarr_utils import load_NgffWellMeta

fractal_tasks_core/tasks/calculate_registration_image_based.py

@@ -18,7 +18,7 @@
 import dask.array as da
 import numpy as np
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 from skimage.registration import phase_cross_correlation
 
 from fractal_tasks_core.channels import get_channel_from_image_zarr

fractal_tasks_core/tasks/cellpose_segmentation.py

@@ -26,8 +26,8 @@
 import pandas as pd
 import zarr
 from cellpose import models
-from pydantic import Field
-from pydantic.decorator import validate_arguments
+from pydantic.v1 import Field
+from pydantic.v1.decorator import validate_arguments
 
 import fractal_tasks_core
 from fractal_tasks_core.labels import prepare_label_group

fractal_tasks_core/tasks/cellpose_utils.py

@@ -16,10 +16,10 @@
 from typing import Optional
 
 import numpy as np
-from pydantic import BaseModel
-from pydantic import Field
-from pydantic import root_validator
-from pydantic import validator
+from pydantic.v1 import BaseModel
+from pydantic.v1 import Field
+from pydantic.v1 import root_validator
+from pydantic.v1 import validator
 
 from fractal_tasks_core.channels import ChannelInputModel
 from fractal_tasks_core.channels import ChannelNotFoundError

fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_compute.py

@@ -18,7 +18,7 @@
 import zarr
 from anndata import read_zarr
 from dask.array.image import imread
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 from fractal_tasks_core.cellvoyager.filenames import (
     glob_with_multiple_patterns,

fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init.py

@@ -17,7 +17,7 @@
 from typing import Optional
 
 import pandas as pd
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 import fractal_tasks_core
 from fractal_tasks_core.cellvoyager.filenames import (

fractal_tasks_core/tasks/cellvoyager_to_ome_zarr_init_multiplex.py

@@ -18,7 +18,7 @@
 
 import pandas as pd
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 from zarr.errors import ContainsGroupError
 
 import fractal_tasks_core

fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py

@@ -16,7 +16,7 @@
 from typing import Any
 
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 import fractal_tasks_core
 from fractal_tasks_core.ngff.specs import NgffPlateMeta

fractal_tasks_core/tasks/find_registration_consensus.py

@@ -17,7 +17,7 @@
 
 import anndata as ad
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 from fractal_tasks_core.roi import (
     are_ROI_table_columns_valid,

fractal_tasks_core/tasks/illumination_correction.py

@@ -22,7 +22,7 @@
 import dask.array as da
 import numpy as np
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 from skimage.io import imread
 
 from fractal_tasks_core.channels import get_omero_channel_list
@@ -106,7 +106,6 @@ def illumination_correction(
     # Advanced parameters
     suffix: str = "_illum_corr",
 ) -> dict[str, Any]:
-
     """
     Applies illumination correction to the images in the OME-Zarr.
 

fractal_tasks_core/tasks/image_based_registration_hcs_init.py

@@ -15,7 +15,7 @@
 import logging
 from typing import Any
 
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 from fractal_tasks_core.tasks._registration_utils import (
     create_well_acquisition_dict,

fractal_tasks_core/tasks/import_ome_zarr.py

@@ -17,7 +17,7 @@
 
 import dask.array as da
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 from fractal_tasks_core.channels import update_omero_channels
 from fractal_tasks_core.ngff import detect_ome_ngff_type

fractal_tasks_core/tasks/init_group_by_well_for_multiplexing.py

@@ -14,7 +14,7 @@
 """
 import logging
 
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 from fractal_tasks_core.tasks._registration_utils import (
     create_well_acquisition_dict,

fractal_tasks_core/tasks/io_models.py

@@ -1,9 +1,9 @@
 from typing import Literal
 from typing import Optional
 
-from pydantic import BaseModel
-from pydantic import Field
-from pydantic import validator
+from pydantic.v1 import BaseModel
+from pydantic.v1 import Field
+from pydantic.v1 import validator
 
 from fractal_tasks_core.channels import ChannelInputModel
 from fractal_tasks_core.channels import OmeroChannel

fractal_tasks_core/tasks/maximum_intensity_projection.py

@@ -18,7 +18,7 @@
 import anndata as ad
 import dask.array as da
 import zarr
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 from zarr.errors import ContainsArrayError
 
 from fractal_tasks_core.ngff import load_NgffImageMeta

fractal_tasks_core/tasks/napari_workflows_wrapper.py

@@ -22,7 +22,7 @@
 import pandas as pd
 import zarr
 from napari_workflows._io_yaml_v1 import load_workflow
-from pydantic.decorator import validate_arguments
+from pydantic.v1.decorator import validate_arguments
 
 import fractal_tasks_core
 from fractal_tasks_core.channels import get_channel_from_image_zarr
@@ -208,7 +208,7 @@ def napari_workflows_wrapper(
     if image_inputs:
         img_array = da.from_zarr(f"{zarr_url}/{level}")
         # Loop over image inputs and assign corresponding channel of the image
-        for (name, params) in image_inputs:
+        for name, params in image_inputs:
             channel = get_channel_from_image_zarr(
                 image_zarr_path=zarr_url,
                 wavelength_id=params.channel.wavelength_id,
@@ -261,7 +261,7 @@ def napari_workflows_wrapper(
             upscale_labels = True
         # Loop over label inputs and load corresponding (upscaled) image
         input_label_arrays = {}
-        for (name, params) in label_inputs:
+        for name, params in label_inputs:
             label_name = params.label_name
             label_array_raw = da.from_zarr(
                 f"{zarr_url}/labels/{label_name}/{level}"
@@ -393,7 +393,7 @@ def napari_workflows_wrapper(
 
         # Loop over label outputs and (1) set zattrs, (2) create zarr group
         output_label_zarr_groups: dict[str, Any] = {}
-        for (name, out_params) in label_outputs:
+        for name, out_params in label_outputs:
 
             # (1a) Rescale OME-NGFF datasets (relevant for level>0)
             if not ngff_image_meta.multiscale.axes[0].name == "c":
@@ -467,7 +467,7 @@ def napari_workflows_wrapper(
         if out_params.type == "dataframe"
     ]
     output_dataframe_lists: dict[str, list] = {}
-    for (name, out_params) in dataframe_outputs:
+    for name, out_params in dataframe_outputs:
         output_dataframe_lists[name] = []
         logger.info(f"Prepared output with {name=} and {out_params=}")
         logger.info(f"{output_dataframe_lists=}")
@@ -581,7 +581,7 @@ def napari_workflows_wrapper(
 
     # Output handling: "dataframe" type (for each output, concatenate ROI
     # dataframes, clean up, and store in a AnnData table on-disk)
-    for (name, out_params) in dataframe_outputs:
+    for name, out_params in dataframe_outputs:
         table_name = out_params.table_name
         # Concatenate all FOV dataframes
         list_dfs = output_dataframe_lists[name]
@@ -617,7 +617,7 @@ def napari_workflows_wrapper(
 
     # Output handling: "label" type (for each output, build and write to disk
     # pyramid of coarser levels)
-    for (name, out_params) in label_outputs:
+    for name, out_params in label_outputs:
         label_name = out_params.label_name
         build_pyramid(
             zarrurl=f"{zarr_url}/labels/{label_name}",