Merge branch 'dev-ilastik-vers' into 'master'

Advanced pinned ilastik version

See merge request !7

svlt-core/requirements.yml

@@ -11,9 +11,8 @@ dependencies:
   - pandas
   - pillow
   - pip
-  - pydantic=1.10.*
+  - pydantic=2.*
   - python=3.9.*
-  - pytorch=1.*
   - scikit-image>=0.21.0
   - tifffile
   - uvicorn>=0.23.0

svlt-core/src/svlt/api.py

@@ -7,7 +7,7 @@ from pydantic import BaseModel, Field
 
 from .accessors import generate_file_accessor, generate_multiposition_file_accessors
 from .models import BinaryThresholdSegmentationModel
-from .pipelines.common import PipelineRecord
+from .pipelines.common import PipelineParams, PipelineRecord
 from .session import session, AccessorIdError, InvalidPathError, WriteAccessorError
 
 app = FastAPI(debug=True)
@@ -185,12 +185,12 @@ def read_multiposition_from_file(filename: str, lazy: bool = False) -> List[str]
 
 class TaskInfo(BaseModel):
     module: str
-    params: dict
+    params: PipelineParams
     func_str: str
     status: str
     target: Union[str, None]
     error: Union[str, None]
-    result: Union[Dict, None]
+    result: Union[PipelineRecord, None]
 
 @app.put('/tasks/run_all')
 def run_all_tasks(write_all: bool = False) -> List[PipelineRecord]:

svlt-core/src/svlt/conf/testing.py

@@ -4,7 +4,10 @@ import unittest
 from math import floor
 from multiprocessing import Process
 from pathlib import Path
+import requests
+from requests.adapters import HTTPAdapter
 from shutil import copyfile
+from urllib3 import Retry
 
 from fastapi import APIRouter
 import numpy as np
@@ -98,8 +101,19 @@ class TestServerBaseClass(unittest.TestCase):
             daemon=True
         )
         self.server_process.start()
+        sesh = requests.Session()
+        retries = Retry(
+            total=10,
+            backoff_factor=0.5,
+        )
+        sesh.mount('http://', requests.adapters.HTTPAdapter(max_retries=retries))
+        resp = sesh.get(f'http://{host}:{int(port):04d}/' + 'status')
+        assert resp.status_code == 200
+
         self.client = HttpClient(host=host, port=port)
 
+
+
     def assertGetSuccess(self, endpoint):
         resp = self.client.get(endpoint)
         self.assertEqual(resp.status_code, 200, resp.text)

svlt-core/src/svlt/pipelines/common.py

@@ -4,7 +4,7 @@ from time import perf_counter
 from typing import Dict, List, Union
 
 from fastapi import HTTPException
-from pydantic import BaseModel, Field, root_validator
+from pydantic import ConfigDict, BaseModel, Field, model_validator
 
 from ..accessors import GenericImageDataAccessor, InMemoryDataAccessor
 from ..session import session, AccessorIdError
@@ -15,31 +15,32 @@ class PipelineParams(BaseModel):
     keep_interm: bool = Field(False, description='Keep accessors to intermediate images in session')
     api: bool = Field(True, description='Validate parameters against server session and map HTTP errors if True')
     calling_task_id: Union[str, None] = Field(None, description='ID of the task that calls pipeline function')
+    model_config = ConfigDict(protected_namespaces = ())
 
-    @root_validator(pre=False)
-    def models_are_loaded(cls, dd):
-        for k, v in dd.items():
-            if dd['api'] and k.endswith('model_id') and v is not None:
+    @model_validator(mode='after')
+    def models_are_loaded(self):
+        for k, v in self.model_dump().items():
+            if self.api and k.endswith('model_id') and v is not None:
                 if v not in session.describe_loaded_models().keys():
                     raise HTTPException(status_code=409, detail=f'Model with {k} = {v} has not been loaded')
-        return dd
+        return self
 
-    @root_validator(pre=False)
-    def accessors_are_loaded(cls, dd):
-        for k, v in dd.items():
-            if dd['api'] and k.endswith('accessor_id'):
+    @model_validator(mode='after')
+    def accessors_are_loaded(self):
+        for k, v in self.model_dump().items():
+            if self.api and k.endswith('accessor_id'):
                 try:
                     info = session.get_accessor_info(v)
                 except AccessorIdError as e:
                     raise HTTPException(status_code=409, detail=str(e))
                 if not session.is_accessor_loaded(v):
                     raise HTTPException(status_code=409, detail=f'Accessor with {k} = {v} has not been loaded')
-        return dd
+        return self
 
 
 class PipelineRecord(BaseModel):
     output_accessor_id: str
-    interm_accessor_ids: Union[Dict[str, str], None]
+    interm_accessor_ids: Union[Dict[str, str], None] = None
     success: bool
     timer: dict
 

svlt-ilastik/requirements.yml

@@ -6,7 +6,7 @@ channels:
 dependencies:
   - czifile
   - fastapi>=0.101
-  - ilastik=1.4.1b6
+  - ilastik=1.4.1b23
   - imagecodecs
   - matplotlib
   - nd2
@@ -14,10 +14,9 @@ dependencies:
   - pandas
   - pillow
   - pip
-  - protobuf ==4.25.3
-  - pydantic=1.10.*
+  - pydantic=2.*
   - python=3.9.*
-  - pytorch=1.*
+  - pytorch
   - scikit-image>=0.21.0
   - scikit-learn>=1.5.0
   - tifffile

svlt-pheno/requirements.yml

@@ -11,7 +11,7 @@ dependencies:
   - pandas
   - pillow
   - pip
-  - pydantic=1.10.*
+  - pydantic=2.*
   - python=3.9.*
   - scikit-image>=0.21.0
   - scikit-learn>=1.5.0