datamint 2.17.2__tar.gz → 2.17.4__tar.gz

{datamint-2.17.2 → datamint-2.17.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: datamint
-Version: 2.17.2
+Version: 2.17.4
 Summary: A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows.
 Requires-Python: >=3.10
 Classifier: Programming Language :: Python :: 3
@@ -9,8 +9,10 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: detection
 Provides-Extra: dev
 Provides-Extra: docs
+Provides-Extra: nnunet
 Requires-Dist: Deprecated (>=1.2.0)
 Requires-Dist: Flask (<4)
 Requires-Dist: Flask-Cors (<7)
@@ -20,6 +22,7 @@ Requires-Dist: albumentations (>=2.0.0)
 Requires-Dist: backports-strenum ; python_version < "3.11"
 Requires-Dist: cachetools (>=6.0.0)
 Requires-Dist: certifi (>=2025.0.0)
+Requires-Dist: filelock (>=3.0) ; extra == "nnunet"
 Requires-Dist: httpx
 Requires-Dist: humanize (>=4.0.0,<5.0.0)
 Requires-Dist: lazy-loader (>=0.3.0)
@@ -29,6 +32,7 @@ Requires-Dist: medimgkit (>=0.17.0)
 Requires-Dist: mlflow-skinny (==3.8.1)
 Requires-Dist: nest-asyncio (>=1.0.0,<2.0.0)
 Requires-Dist: nibabel (>=4.0.0)
+Requires-Dist: nnunetv2 (>=2.4,<3.0) ; extra == "nnunet"
 Requires-Dist: numpy
 Requires-Dist: opencv-python (>=4.0.0)
 Requires-Dist: pandas (>=2.0.0)
@@ -53,6 +57,7 @@ Requires-Dist: torch (>=1.2.0,!=2.3.0)
 Requires-Dist: torchvision (>=0.18.0)
 Requires-Dist: tqdm (>=4.0.0,<5.0.0)
 Requires-Dist: typing_extensions (>=4.0.0)
+Requires-Dist: yolox-datamint (>=0.3.1) ; extra == "detection"
 Description-Content-Type: text/markdown
 
 # Datamint Python API
@@ -176,6 +181,14 @@ datamint-upload /path/to/dicoms \
 ```
 Use `--ai-model` when uploaded segmentation files should be linked to an existing deployed model by name. `--segmentation_names` accepts YAML mappings and ITK-SNAP label export CSV/TXT files.
 
+### Scaffold a New Project
+
+```bash
+datamint-init
+```
+
+Generates a numbered set of scripts (`01_upload_data.py` through `06_deploy.py`) for your task (detection, segmentation, or classification). Run it once in a new directory and follow the scripts in order.
+
 ### Configuration Management
 
 ```bash
@@ -230,7 +243,7 @@ api = Api(verify_ssl=False)
 
 ## 🆘 Support
 
-[Full Documentation](https://datamint-python-api.readthedocs.io/)  
+[Full Documentation](https://sonanceai.github.io/datamint-python-api)  
 [GitHub Issues](https://github.com/SonanceAI/datamint-python-api/issues)
 
 

{datamint-2.17.2 → datamint-2.17.4}/README.md

@@ -119,6 +119,14 @@ datamint-upload /path/to/dicoms \
 ```
 Use `--ai-model` when uploaded segmentation files should be linked to an existing deployed model by name. `--segmentation_names` accepts YAML mappings and ITK-SNAP label export CSV/TXT files.
 
+### Scaffold a New Project
+
+```bash
+datamint-init
+```
+
+Generates a numbered set of scripts (`01_upload_data.py` through `06_deploy.py`) for your task (detection, segmentation, or classification). Run it once in a new directory and follow the scripts in order.
+
 ### Configuration Management
 
 ```bash
@@ -173,6 +181,6 @@ api = Api(verify_ssl=False)
 
 ## 🆘 Support
 
-[Full Documentation](https://datamint-python-api.readthedocs.io/)  
+[Full Documentation](https://sonanceai.github.io/datamint-python-api)  
 [GitHub Issues](https://github.com/SonanceAI/datamint-python-api/issues)
 

{datamint-2.17.2 → datamint-2.17.4}/datamint/__init__.py

@@ -9,7 +9,8 @@ if TYPE_CHECKING:
     # New modular datasets
     from .dataset.image_dataset import ImageDataset
     from .dataset.volume_dataset import VolumeDataset
-    
+    from .mlflow.flavors.validation import validate_model, ValidationReport, ValidationIssue, ModelValidationError
+
 else:
     import lazy_loader as lazy
 
@@ -21,6 +22,8 @@ else:
             # New modular dataset classes
             "dataset.image_dataset": ["ImageDataset"],
             "dataset.volume_dataset": ["VolumeDataset"],
+            "mlflow.flavors.validation": ["validate_model", "ValidationReport",
+                                          "ValidationIssue", "ModelValidationError"],
         },
     )
 

{datamint-2.17.2 → datamint-2.17.4}/datamint/api/base_api.py

@@ -3,7 +3,14 @@ from typing import TYPE_CHECKING
 from collections.abc import Generator, AsyncGenerator
 import httpx
 from dataclasses import dataclass
-from datamint.exceptions import DatamintException, ItemNotFoundError
+from datamint.exceptions import (
+    ItemNotFoundError,
+    AuthenticationError,
+    PermissionDeniedError,
+    ValidationError,
+    NetworkError,
+    ServerError,
+)
 import aiohttp
 import json
 from PIL import Image
@@ -126,7 +133,7 @@ class BaseApi:
             original_error: The original SSL-related exception
 
         Raises:
-            DatamintException: With helpful troubleshooting information
+            NetworkError: With helpful troubleshooting information
         """
         error_msg = (
             f"SSL Certificate verification failed: {original_error}\n\n"
@@ -141,7 +148,7 @@ class BaseApi:
             "   api = Api(verify_ssl=False)\n\n"
             "For more help, see: https://github.com/SonanceAI/datamint-python-api#-ssl-certificate-troubleshooting"
         )
-        raise DatamintException(error_msg) from original_error
+        raise NetworkError(error_msg) from original_error
 
     def _create_aiohttp_connector(self, force_close: bool = False) -> aiohttp.TCPConnector:
         """Create aiohttp connector with SSL configuration.
@@ -417,7 +424,7 @@ class BaseApi:
         except httpx.ConnectError as e:
             if "CERTIFICATE_VERIFY_FAILED" in str(e) or "certificate verify failed" in str(e).lower():
                 self._raise_ssl_error(e)
-            raise
+            raise NetworkError(str(e)) from e
         except httpx.HTTPError as e:
             try:
                 response_json = response.json()
@@ -426,18 +433,21 @@ class BaseApi:
             error_msg = f"{getattr(e, 'message', str(e))} | {getattr(response, 'text', '')}"
             if response_json:
                 error_msg = f"{error_msg} | {response_json}"
-            try:
-                e.message = error_msg
-            except Exception:
-                logger.debug("Unable to set message attribute on exception")
-                pass
 
             status_code = response.status_code
-            if status_code in (400, 404):
+            if status_code == 401:
+                raise AuthenticationError(error_msg) from e
+            if status_code == 403:
+                raise PermissionDeniedError(error_msg) from e
+            if status_code in (400, 422):
+                raise ValidationError(error_msg) from e
+            if status_code == 404:
                 new_error_msg = error_msg.replace('404 Not Found', '')
                 if ' not found' in new_error_msg.lower() or 'Not Found' in new_error_msg:
-                    # Will be caught by the caller and properly initialized:
                     raise ItemNotFoundError('unknown', {})
+                raise ValidationError(error_msg) from e
+            if status_code >= 500:
+                raise ServerError(error_msg, status_code=status_code) from e
             raise
         return response_json
 
@@ -447,9 +457,10 @@ class BaseApi:
         response_json = None
         try:
             response.raise_for_status()
+        except aiohttp.ClientConnectionError as e:
+            raise NetworkError(str(e)) from e
         except aiohttp.ClientError as e:
             error_msg = str(getattr(e, 'message', e))
-            # log the raw response for debugging
             status_code = BaseApi.get_status_code(e)
             # Only read the body on error to get detailed message; do NOT read on success
             # as that would exhaust the stream before callers can iterate over it.
@@ -461,15 +472,18 @@ class BaseApi:
                 error_msg = f"{error_msg} | {response_json}"
 
             logger.error(f"HTTP error {status_code} for {url}: {error_msg}")
-            try:
-                e.message = error_msg
-            except Exception:
-                logger.debug("Unable to set message attribute on exception")
-                pass
-            if status_code in (400, 404):
+            if status_code == 401:
+                raise AuthenticationError(error_msg) from e
+            if status_code == 403:
+                raise PermissionDeniedError(error_msg) from e
+            if status_code in (400, 422):
+                raise ValidationError(error_msg) from e
+            if status_code == 404:
                 if ' not found' in error_msg.lower() or 'Not Found' in error_msg:
-                    # Will be caught by the caller and properly initialized:
                     raise ItemNotFoundError('unknown', {})
+                raise ValidationError(error_msg) from e
+            if status_code >= 500:
+                raise ServerError(error_msg, status_code=status_code) from e
             raise
         return response_json
 

{datamint-2.17.2 → datamint-2.17.4}/datamint/api/client.py

@@ -6,7 +6,7 @@ from .endpoints import (ProjectsApi, ResourcesApi, AnnotationsApi,
                         )
 from .endpoints.models_api import ModelsApi
 import datamint.configs
-from datamint.exceptions import DatamintException
+from datamint.exceptions import AuthenticationError, NetworkError
 import logging
 
 _LOGGER = logging.getLogger(__name__)
@@ -58,7 +58,7 @@ class Api:
             if api_key is None:
                 msg = f"API key not provided! Use the environment variable " + \
                     f"{Api.DATAMINT_API_VENV_NAME} or pass it as an argument."
-                raise DatamintException(msg)
+                raise AuthenticationError(msg)
         self.config = ApiConfig(
             server_url=server_url,
             api_key=api_key,
@@ -94,8 +94,8 @@ class Api:
         try:
             self.projects.get_list(limit=1)
         except Exception as e:
-            raise DatamintException("Error connecting to the Datamint API." +
-                                    f" Please check your api_key and/or other configurations.") from e
+            raise NetworkError("Error connecting to the Datamint API."
+                               " Please check your api_key and/or other configurations.") from e
 
     def close(self) -> None:
         """Close underlying HTTP clients and any shared aiohttp sessions.

{datamint-2.17.2 → datamint-2.17.4}/datamint/api/endpoints/annotations_api.py

@@ -31,7 +31,7 @@ from datamint.entities.annotations import (
     LineAnnotation,
     annotation_from_dict,
 )
-from datamint.exceptions import DatamintException, ItemNotFoundError
+from datamint.exceptions import ItemNotFoundError, ServerError
 from datamint.utils.nifti_utils import metadata_to_nifti_obj
 
 from ..entity_base_api import ApiConfig, CreatableEntityApi, DeletableEntityApi
@@ -453,7 +453,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                       the basename of the path will be used.
 
         Raises:
-            DatamintException: If the upload fails.
+            ServerError: If the upload fails.
 
         """
         f, filename, close_file, content_type = self._prepare_upload_file(file,
@@ -470,7 +470,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                                                            session=session,
                                                            data=form)
             if isinstance(respdata, dict) and 'error' in respdata:
-                raise DatamintException(respdata['error'])
+                raise ServerError(respdata['error'])
         finally:
             if close_file:
                 f.close()
@@ -494,7 +494,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                       the basename of the path will be used.
 
         Raises:
-            DatamintException: If the upload fails.
+            ServerError: If the upload fails.
         """
         f, filename, close_file, content_type = self._prepare_upload_file(file,
                                                                           filename,
@@ -509,7 +509,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                                       files=files)
             respdata = resp.json()
             if isinstance(respdata, dict) and 'error' in respdata:
-                raise DatamintException(respdata['error'])
+                raise ServerError(respdata['error'])
         finally:
             if close_file:
                 f.close()
@@ -550,7 +550,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                                       json=annotations_payload).json()
         for r in respdata:
             if isinstance(r, dict) and 'error' in r:
-                raise DatamintException(r['error'])
+                raise ServerError(r['error'])
         if is_single_annotation:
             return respdata[0]
         return respdata
@@ -788,7 +788,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                                                        json=annotations)
         for r in respdata:
             if isinstance(r, dict) and 'error' in r:
-                raise DatamintException(r['error'])
+                raise ServerError(r['error'])
         return respdata
 
     @staticmethod
@@ -917,7 +917,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                         raise
 
                     if 'error' in respdata:
-                        raise DatamintException(respdata['error'])
+                        raise ServerError(respdata['error'])
                     return respdata
             else:
                 raise ValueError(f"Volume upload not supported for file format: {file_path}")
@@ -951,7 +951,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
                 raise
 
             if 'error' in respdata:
-                raise DatamintException(respdata['error'])
+                raise ServerError(respdata['error'])
             return respdata
         else:
             raise ValueError(f"Unsupported file_path type for volume upload: {type(file_path)}")
@@ -1460,7 +1460,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
             project_id: Optional project ID to associate with the annotation.
 
         Raises:
-            DatamintException: If the update fails.
+            ServerError: If the update fails.
         """
         annotation_id = self._entid(annotation)
 
@@ -1477,7 +1477,7 @@ class AnnotationsApi(CreatableEntityApi[Annotation], DeletableEntityApi[Annotati
 
         respdata = resp.json()
         if isinstance(respdata, dict) and 'error' in respdata:
-            raise DatamintException(respdata['error'])
+            raise ServerError(respdata['error'])
 
     def approve(self, annotation: str | Annotation) -> None:
         """Approve an annotation.