Switch to Pydantic V2? #5
Comments
5 tasks
|
Thanks for the heads up @tcompa. I tried to update everything to pydantic v2.0 on https://github.com/Apricot-Therapeutics/APx_fractal_task_collection/tree/pydantic_v2. Works for me locally, let me know if something is still wrong. |
It does work, thanks! First, our GitHub Action now runs successfully: https://github.com/fractal-analytics-platform/fractal-tasks-core/actions/runs/10037714190/job/27738094738?pr=793. Second, I cloned the apx repo to review how the manifest is changing. The diff output is below. Apart from the diff --git a/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json b/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json
index c7fe603..51c7486 100644
--- a/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json
+++ b/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json
@@ -1,22 +1,21 @@
{
- "args_schema_version": "pydantic_v1",
+ "args_schema_version": "pydantic_v2",
"has_args_schemas": true,
"manifest_version": "2",
"task_list": [
{
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"ChannelInputModel": {
"description": "A channel which is specified by either `wavelength_id` or `label`.",
"properties": {
"label": {
- "description": "Name of the channel.",
+ "description": "Name of the channel. Can only be specified if wavelength_id is not set.",
"title": "Label",
"type": "string"
},
"wavelength_id": {
- "description": "Unique ID for the channel wavelength, e.g. `A01_C01`.",
+ "description": "Unique ID for the channel wavelength, e.g. `A01_C01`. Can only be specified if label is not set.",
"title": "Wavelength Id",
"type": "string"
}
@@ -55,6 +54,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"ROI_table_name": {
"description": "Missing description",
@@ -70,7 +70,7 @@
"channels_to_exclude": {
"description": "List of channels to exclude for intensity and texture measurements. Use the channel label to indicate single channels. If None, no channels are excluded.",
"items": {
- "$ref": "#/definitions/ChannelInputModel"
+ "$ref": "#/$defs/ChannelInputModel"
},
"title": "Channels To Exclude",
"type": "array"
@@ -78,7 +78,7 @@
"channels_to_include": {
"description": "List of channels to include for intensity and texture measurements. Use the channel label to indicate single channels. If None, all channels are included.",
"items": {
- "$ref": "#/definitions/ChannelInputModel"
+ "$ref": "#/$defs/ChannelInputModel"
},
"title": "Channels To Include",
"type": "array"
@@ -115,7 +115,7 @@
"measure_texture": {
"allOf": [
{
- "$ref": "#/definitions/TextureFeatures"
+ "$ref": "#/$defs/TextureFeatures"
}
],
"default": {
@@ -210,8 +210,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsSegmentSecondary": {
"description": "Segment Secondary HCS Plate init args.",
"properties": {
@@ -250,6 +249,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"ROI_table_name": {
"description": "Name of the table containing the ROIs.",
@@ -273,9 +273,9 @@
"type": "integer"
},
"init_args": {
- "$ref": "#/definitions/InitArgsSegmentSecondary",
+ "$ref": "#/$defs/InitArgsSegmentSecondary",
"description": "Intialization arguments provided by `init_segment_secondary_objects`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -330,15 +330,14 @@
},
{
"args_schema_non_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"MultiplexingAcquisition": {
"description": "Input class for Multiplexing Cellvoyager converter",
"properties": {
"allowed_channels": {
"description": "A list of `OmeroChannel` objects, where each channel must include the `wavelength_id` attribute and where the `wavelength_id` values must be unique across the list.",
"items": {
- "$ref": "#/definitions/OmeroChannel"
+ "$ref": "#/$defs/OmeroChannel"
},
"title": "Allowed Channels",
"type": "array"
@@ -398,7 +397,11 @@
"type": "string"
},
"window": {
- "$ref": "#/definitions/Window",
+ "allOf": [
+ {
+ "$ref": "#/$defs/Window"
+ }
+ ],
"description": "Optional `Window` object to set default display settings for napari.",
"title": "Window"
}
@@ -441,10 +444,11 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"acquisitions": {
"additionalProperties": {
- "$ref": "#/definitions/MultiplexingAcquisition"
+ "$ref": "#/$defs/MultiplexingAcquisition"
},
"description": "dictionary of acquisitions. Each key is the acquisition identifier (normally 0, 1, 2, 3 etc.). Each item defines the acquisition by providing the image_dir and the allowed_channels.",
"title": "Acquisitions",
@@ -505,8 +509,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsIC6000": {
"description": "Arguments to be passed from IC6000 converter init to compute",
"properties": {
@@ -542,17 +545,20 @@
"image_dir",
"plate_prefix",
"well_ID",
- "image_extension"
+ "image_extension",
+ "image_glob_patterns",
+ "acquisition"
],
"title": "InitArgsIC6000",
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsIC6000",
+ "$ref": "#/$defs/InitArgsIC6000",
"description": "Intialization arguments provided by `init_convert_IC600_to_ome_zarr`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"zarr_url": {
"description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server).",
@@ -614,8 +620,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsLabelAssignment": {
"description": "Arguments to be passed from Label Assignment init to compute",
"properties": {
@@ -646,6 +651,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"child_table_name": {
"description": "Name of the feature table associated with the child label image.",
@@ -653,9 +659,9 @@
"type": "string"
},
"init_args": {
- "$ref": "#/definitions/InitArgsLabelAssignment",
+ "$ref": "#/$defs/InitArgsLabelAssignment",
"description": "Intialization arguments provided by `init_label_assignment_by_overlap`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -736,8 +742,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsClipLabelImage": {
"description": "Arguments to be passed from Clip Label Image init to compute",
"properties": {
@@ -768,11 +773,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsClipLabelImage",
+ "$ref": "#/$defs/InitArgsClipLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -858,8 +864,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsMaskLabelImage": {
"description": "Arguments to be passed from Mask Label Image init to compute",
"properties": {
@@ -890,11 +895,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsMaskLabelImage",
+ "$ref": "#/$defs/InitArgsMaskLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -974,8 +980,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsFilterLabelBySize": {
"description": "Arguments to be passed from Filter Label by Size init to compute",
"properties": {
@@ -996,11 +1001,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsFilterLabelBySize",
+ "$ref": "#/$defs/InitArgsFilterLabelBySize",
"description": "Intialization arguments provided by `init_filter_label_by_size`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -1090,8 +1096,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsBaSiCPyCalculate": {
"description": "Arguments to be passed from BaSiCPy Calculate init to compute",
"properties": {
@@ -1128,6 +1133,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"illumination_profiles_folder": {
"description": "Path to folder where illumination profiles will be saved.",
@@ -1135,9 +1141,9 @@
"type": "string"
},
"init_args": {
- "$ref": "#/definitions/InitArgsBaSiCPyCalculate",
+ "$ref": "#/$defs/InitArgsBaSiCPyCalculate",
"description": "Intialization arguments provided by `init_calculate_basicpy_illumination_models`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite": {
"default": false,
@@ -1256,8 +1262,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsAggregateFeatureTables": {
"description": "Arguments to be passed from BaSiCPy Calculate init to compute",
"properties": {
@@ -1276,11 +1281,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsAggregateFeatureTables",
+ "$ref": "#/$defs/InitArgsAggregateFeatureTables",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"input_table_name": {
"description": "Name of the feature table.",
@@ -1544,8 +1550,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsCorrectChromaticShift": {
"description": "Arguments to be passed from Correct Chromatic Shift init to compute",
"properties": {
@@ -1572,11 +1577,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsCorrectChromaticShift",
+ "$ref": "#/$defs/InitArgsCorrectChromaticShift",
"description": "Intialization arguments provided by `init_correct_chromatic_shift.py`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite_input": {
"default": true,
@@ -1656,8 +1662,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsConvertChannelToLabel": {
"description": "Arguments to be passed from Convert Channel to Label init to compute",
"properties": {
@@ -1678,11 +1683,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsConvertChannelToLabel",
+ "$ref": "#/$defs/InitArgsConvertChannelToLabel",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"output_label_name": {
"description": "Missing description",
@@ -1756,8 +1762,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsDetectBlobCentroids": {
"description": "Arguments to be passed from Convert Channel to Label init to compute",
"properties": {
@@ -1778,6 +1783,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"ROI_table_name": {
"description": "Name of the table containing the ROIs.",
@@ -1785,9 +1791,9 @@
"type": "string"
},
"init_args": {
- "$ref": "#/definitions/InitArgsDetectBlobCentroids",
+ "$ref": "#/$defs/InitArgsDetectBlobCentroids",
"description": "Intialization arguments provided by `init_detect_blob_centroids`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -1863,24 +1869,23 @@
]
}
{
- "args_schema_version": "pydantic_v1",
+ "args_schema_version": "pydantic_v2",
"has_args_schemas": true,
"manifest_version": "2",
"task_list": [
{
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"ChannelInputModel": {
"description": "A channel which is specified by either `wavelength_id` or `label`.",
"properties": {
"label": {
- "description": "Name of the channel.",
+ "description": "Name of the channel. Can only be specified if wavelength_id is not set.",
"title": "Label",
"type": "string"
},
"wavelength_id": {
- "description": "Unique ID for the channel wavelength, e.g. `A01_C01`.",
+ "description": "Unique ID for the channel wavelength, e.g. `A01_C01`. Can only be specified if label is not set.",
"title": "Wavelength Id",
"type": "string"
}
@@ -1919,6 +1924,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"ROI_table_name": {
"description": "Missing description",
@@ -1934,7 +1940,7 @@
"channels_to_exclude": {
"description": "List of channels to exclude for intensity and texture measurements. Use the channel label to indicate single channels. If None, no channels are excluded.",
"items": {
- "$ref": "#/definitions/ChannelInputModel"
+ "$ref": "#/$defs/ChannelInputModel"
},
"title": "Channels To Exclude",
"type": "array"
@@ -1942,7 +1948,7 @@
"channels_to_include": {
"description": "List of channels to include for intensity and texture measurements. Use the channel label to indicate single channels. If None, all channels are included.",
"items": {
- "$ref": "#/definitions/ChannelInputModel"
+ "$ref": "#/$defs/ChannelInputModel"
},
"title": "Channels To Include",
"type": "array"
@@ -1979,7 +1985,7 @@
"measure_texture": {
"allOf": [
{
- "$ref": "#/definitions/TextureFeatures"
+ "$ref": "#/$defs/TextureFeatures"
}
],
"default": {
@@ -2074,8 +2080,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsSegmentSecondary": {
"description": "Segment Secondary HCS Plate init args.",
"properties": {
@@ -2114,6 +2119,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"ROI_table_name": {
"description": "Name of the table containing the ROIs.",
@@ -2137,9 +2143,9 @@
"type": "integer"
},
"init_args": {
- "$ref": "#/definitions/InitArgsSegmentSecondary",
+ "$ref": "#/$defs/InitArgsSegmentSecondary",
"description": "Intialization arguments provided by `init_segment_secondary_objects`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2194,15 +2200,14 @@
},
{
"args_schema_non_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"MultiplexingAcquisition": {
"description": "Input class for Multiplexing Cellvoyager converter",
"properties": {
"allowed_channels": {
"description": "A list of `OmeroChannel` objects, where each channel must include the `wavelength_id` attribute and where the `wavelength_id` values must be unique across the list.",
"items": {
- "$ref": "#/definitions/OmeroChannel"
+ "$ref": "#/$defs/OmeroChannel"
},
"title": "Allowed Channels",
"type": "array"
@@ -2262,7 +2267,11 @@
"type": "string"
},
"window": {
- "$ref": "#/definitions/Window",
+ "allOf": [
+ {
+ "$ref": "#/$defs/Window"
+ }
+ ],
"description": "Optional `Window` object to set default display settings for napari.",
"title": "Window"
}
@@ -2305,10 +2314,11 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"acquisitions": {
"additionalProperties": {
- "$ref": "#/definitions/MultiplexingAcquisition"
+ "$ref": "#/$defs/MultiplexingAcquisition"
},
"description": "dictionary of acquisitions. Each key is the acquisition identifier (normally 0, 1, 2, 3 etc.). Each item defines the acquisition by providing the image_dir and the allowed_channels.",
"title": "Acquisitions",
@@ -2369,8 +2379,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsIC6000": {
"description": "Arguments to be passed from IC6000 converter init to compute",
"properties": {
@@ -2406,17 +2415,20 @@
"image_dir",
"plate_prefix",
"well_ID",
- "image_extension"
+ "image_extension",
+ "image_glob_patterns",
+ "acquisition"
],
"title": "InitArgsIC6000",
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsIC6000",
+ "$ref": "#/$defs/InitArgsIC6000",
"description": "Intialization arguments provided by `init_convert_IC600_to_ome_zarr`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"zarr_url": {
"description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server).",
@@ -2478,8 +2490,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsLabelAssignment": {
"description": "Arguments to be passed from Label Assignment init to compute",
"properties": {
@@ -2510,6 +2521,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"child_table_name": {
"description": "Name of the feature table associated with the child label image.",
@@ -2517,9 +2529,9 @@
"type": "string"
},
"init_args": {
- "$ref": "#/definitions/InitArgsLabelAssignment",
+ "$ref": "#/$defs/InitArgsLabelAssignment",
"description": "Intialization arguments provided by `init_label_assignment_by_overlap`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2600,8 +2612,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsClipLabelImage": {
"description": "Arguments to be passed from Clip Label Image init to compute",
"properties": {
@@ -2632,11 +2643,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsClipLabelImage",
+ "$ref": "#/$defs/InitArgsClipLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2722,8 +2734,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsMaskLabelImage": {
"description": "Arguments to be passed from Mask Label Image init to compute",
"properties": {
@@ -2754,11 +2765,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsMaskLabelImage",
+ "$ref": "#/$defs/InitArgsMaskLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2838,8 +2850,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsFilterLabelBySize": {
"description": "Arguments to be passed from Filter Label by Size init to compute",
"properties": {
@@ -2860,11 +2871,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsFilterLabelBySize",
+ "$ref": "#/$defs/InitArgsFilterLabelBySize",
"description": "Intialization arguments provided by `init_filter_label_by_size`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2954,8 +2966,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsBaSiCPyCalculate": {
"description": "Arguments to be passed from BaSiCPy Calculate init to compute",
"properties": {
@@ -2992,6 +3003,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"illumination_profiles_folder": {
"description": "Path to folder where illumination profiles will be saved.",
@@ -2999,9 +3011,9 @@
"type": "string"
},
"init_args": {
- "$ref": "#/definitions/InitArgsBaSiCPyCalculate",
+ "$ref": "#/$defs/InitArgsBaSiCPyCalculate",
"description": "Intialization arguments provided by `init_calculate_basicpy_illumination_models`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite": {
"default": false,
@@ -3120,8 +3132,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsAggregateFeatureTables": {
"description": "Arguments to be passed from BaSiCPy Calculate init to compute",
"properties": {
@@ -3140,11 +3151,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsAggregateFeatureTables",
+ "$ref": "#/$defs/InitArgsAggregateFeatureTables",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"input_table_name": {
"description": "Name of the feature table.",
@@ -3408,8 +3420,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsCorrectChromaticShift": {
"description": "Arguments to be passed from Correct Chromatic Shift init to compute",
"properties": {
@@ -3436,11 +3447,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsCorrectChromaticShift",
+ "$ref": "#/$defs/InitArgsCorrectChromaticShift",
"description": "Intialization arguments provided by `init_correct_chromatic_shift.py`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite_input": {
"default": true,
@@ -3520,8 +3532,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsConvertChannelToLabel": {
"description": "Arguments to be passed from Convert Channel to Label init to compute",
"properties": {
@@ -3542,11 +3553,12 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"init_args": {
- "$ref": "#/definitions/InitArgsConvertChannelToLabel",
+ "$ref": "#/$defs/InitArgsConvertChannelToLabel",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"output_label_name": {
"description": "Missing description",
@@ -3620,8 +3632,7 @@
"type": "object"
},
"args_schema_parallel": {
- "additionalProperties": false,
- "definitions": {
+ "$defs": {
"InitArgsDetectBlobCentroids": {
"description": "Arguments to be passed from Convert Channel to Label init to compute",
"properties": {
@@ -3642,6 +3653,7 @@
"type": "object"
}
},
+ "additionalProperties": false,
"properties": {
"ROI_table_name": {
"description": "Name of the table containing the ROIs.",
@@ -3649,9 +3661,9 @@
"type": "string"
},
"init_args": {
- "$ref": "#/definitions/InitArgsDetectBlobCentroids",
+ "$ref": "#/$defs/InitArgsDetectBlobCentroids",
"description": "Intialization arguments provided by `init_detect_blob_centroids`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0, |
|
As a second check, I replaced And here is the (more readable) output diff --git a/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json b/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json
index c7fe603..54ca130 100644
--- a/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json
+++ b/src/apx_fractal_task_collection/__FRACTAL_MANIFEST__.json
@@ -1,5 +1,5 @@
{
- "args_schema_version": "pydantic_v1",
+ "args_schema_version": "pydantic_v2",
"has_args_schemas": true,
"manifest_version": "2",
"task_list": [
@@ -11,12 +11,12 @@
"description": "A channel which is specified by either `wavelength_id` or `label`.",
"properties": {
"label": {
- "description": "Name of the channel.",
+ "description": "Name of the channel. Can only be specified if wavelength_id is not set.",
"title": "Label",
"type": "string"
},
"wavelength_id": {
- "description": "Unique ID for the channel wavelength, e.g. `A01_C01`.",
+ "description": "Unique ID for the channel wavelength, e.g. `A01_C01`. Can only be specified if label is not set.",
"title": "Wavelength Id",
"type": "string"
}
@@ -275,7 +275,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsSegmentSecondary",
"description": "Intialization arguments provided by `init_segment_secondary_objects`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -398,7 +398,11 @@
"type": "string"
},
"window": {
- "$ref": "#/definitions/Window",
+ "allOf": [
+ {
+ "$ref": "#/definitions/Window"
+ }
+ ],
"description": "Optional `Window` object to set default display settings for napari.",
"title": "Window"
}
@@ -542,7 +546,9 @@
"image_dir",
"plate_prefix",
"well_ID",
- "image_extension"
+ "image_extension",
+ "image_glob_patterns",
+ "acquisition"
],
"title": "InitArgsIC6000",
"type": "object"
@@ -552,7 +558,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsIC6000",
"description": "Intialization arguments provided by `init_convert_IC600_to_ome_zarr`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"zarr_url": {
"description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server).",
@@ -655,7 +661,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsLabelAssignment",
"description": "Intialization arguments provided by `init_label_assignment_by_overlap`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -772,7 +778,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsClipLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -894,7 +900,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsMaskLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -1000,7 +1006,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsFilterLabelBySize",
"description": "Intialization arguments provided by `init_filter_label_by_size`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -1137,7 +1143,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsBaSiCPyCalculate",
"description": "Intialization arguments provided by `init_calculate_basicpy_illumination_models`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite": {
"default": false,
@@ -1280,7 +1286,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsAggregateFeatureTables",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"input_table_name": {
"description": "Name of the feature table.",
@@ -1576,7 +1582,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsCorrectChromaticShift",
"description": "Intialization arguments provided by `init_correct_chromatic_shift.py`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite_input": {
"default": true,
@@ -1682,7 +1688,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsConvertChannelToLabel",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"output_label_name": {
"description": "Missing description",
@@ -1787,7 +1793,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsDetectBlobCentroids",
"description": "Intialization arguments provided by `init_detect_blob_centroids`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -1863,7 +1869,7 @@
]
}
{
- "args_schema_version": "pydantic_v1",
+ "args_schema_version": "pydantic_v2",
"has_args_schemas": true,
"manifest_version": "2",
"task_list": [
@@ -1875,12 +1881,12 @@
"description": "A channel which is specified by either `wavelength_id` or `label`.",
"properties": {
"label": {
- "description": "Name of the channel.",
+ "description": "Name of the channel. Can only be specified if wavelength_id is not set.",
"title": "Label",
"type": "string"
},
"wavelength_id": {
- "description": "Unique ID for the channel wavelength, e.g. `A01_C01`.",
+ "description": "Unique ID for the channel wavelength, e.g. `A01_C01`. Can only be specified if label is not set.",
"title": "Wavelength Id",
"type": "string"
}
@@ -2139,7 +2145,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsSegmentSecondary",
"description": "Intialization arguments provided by `init_segment_secondary_objects`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2262,7 +2268,11 @@
"type": "string"
},
"window": {
- "$ref": "#/definitions/Window",
+ "allOf": [
+ {
+ "$ref": "#/definitions/Window"
+ }
+ ],
"description": "Optional `Window` object to set default display settings for napari.",
"title": "Window"
}
@@ -2406,7 +2416,9 @@
"image_dir",
"plate_prefix",
"well_ID",
- "image_extension"
+ "image_extension",
+ "image_glob_patterns",
+ "acquisition"
],
"title": "InitArgsIC6000",
"type": "object"
@@ -2416,7 +2428,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsIC6000",
"description": "Intialization arguments provided by `init_convert_IC600_to_ome_zarr`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"zarr_url": {
"description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server).",
@@ -2519,7 +2531,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsLabelAssignment",
"description": "Intialization arguments provided by `init_label_assignment_by_overlap`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2636,7 +2648,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsClipLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2758,7 +2770,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsMaskLabelImage",
"description": "Intialization arguments provided by `init_clip_label_image`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -2864,7 +2876,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsFilterLabelBySize",
"description": "Intialization arguments provided by `init_filter_label_by_size`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0,
@@ -3001,7 +3013,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsBaSiCPyCalculate",
"description": "Intialization arguments provided by `init_calculate_basicpy_illumination_models`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite": {
"default": false,
@@ -3144,7 +3156,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsAggregateFeatureTables",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"input_table_name": {
"description": "Name of the feature table.",
@@ -3440,7 +3452,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsCorrectChromaticShift",
"description": "Intialization arguments provided by `init_correct_chromatic_shift.py`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"overwrite_input": {
"default": true,
@@ -3546,7 +3558,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsConvertChannelToLabel",
"description": "Missing description",
- "title": "Init_Args"
+ "title": "Init Args"
},
"output_label_name": {
"description": "Missing description",
@@ -3651,7 +3663,7 @@
"init_args": {
"$ref": "#/definitions/InitArgsDetectBlobCentroids",
"description": "Intialization arguments provided by `init_detect_blob_centroids`.",
- "title": "Init_Args"
+ "title": "Init Args"
},
"level": {
"default": 0, |
|
TL;DR |
|
Thanks for running the additional checks. Will keep an eye on the PR! |
Merged
|
You may want to update your dependency to fractal-tasks-core 1.2.0, which is now fully using pydantic v2. (and feel free to report any unexpected behavior..) |
|
Thanks for the update, apx_fractal_tasks_collection main now has all the pydantic v2 changes. |
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One of the upcoming
fractal-tasks-corereleases will depend onpydantic>=2. Using this newfractal-tasks-coreversion for generating the manifest ofAPx_fractal_task_collectioncurrently fails, probably because some Pydantic V1 parts of APx should be updated to work with Pydantic v2 -- see below.This is the failing CI workflow: https://github.com/fractal-analytics-platform/fractal-tasks-core/actions/runs/10006172758/job/27658348914?pr=793.
And here is the relevant bit of traceback for
python src/apx_fractal_task_collection/dev/update_manifest.py(which points to https://docs.pydantic.dev/2.8/errors/usage_errors/#root-validator-pre-skip):The text was updated successfully, but these errors were encountered: