datamint 1.2.4__tar.gz → 1.3.0__tar.gz

{datamint-1.2.4 → datamint-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: datamint
-Version: 1.2.4
+Version: 1.3.0
 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
@@ -14,6 +14,7 @@ Requires-Dist: Deprecated (>=1.2.0)
 Requires-Dist: aiohttp (>=3.0.0,<4.0.0)
 Requires-Dist: aioresponses (>=0.7.8,<0.8.0) ; extra == "dev"
 Requires-Dist: albumentations (>=2.0.0)
+Requires-Dist: datamintapi (==0.0.*)
 Requires-Dist: humanize (>=4.0.0,<5.0.0)
 Requires-Dist: lazy-loader (>=0.3.0)
 Requires-Dist: lightning
@@ -52,13 +53,12 @@ See the full documentation at https://sonanceai.github.io/datamint-python-api/
 ## Installation
 
 Datamint requires Python 3.10+.
-You can install Datamint and its dependencies using pip
+You can install/update Datamint and its dependencies using pip
 
 ```bash
-pip install git+https://github.com/SonanceAI/datamint-python-api
+pip install -U datamint
 ```
 
-Soon we will be releasing the package on PyPi.
 We recommend that you install Datamint in a dedicated virtual environment, to avoid conflicting with your system packages.
 Create the enviroment once with `python3 -m venv datamint-env` and then activate it whenever you need it with:
 - `source datamint-env/bin/activate` (Linux/MAC)
@@ -95,7 +95,7 @@ os.environ["DATAMINT_API_KEY"] = "my_api_key"
 Specify API key in the |APIHandlerClass| constructor:
 
 ```python
-from datamintapi import APIHandler
+from datamint import APIHandler
 api = APIHandler(api_key='my_api_key')
 ```
 

{datamint-1.2.4 → datamint-1.3.0}/README.md

@@ -8,13 +8,12 @@ See the full documentation at https://sonanceai.github.io/datamint-python-api/
 ## Installation
 
 Datamint requires Python 3.10+.
-You can install Datamint and its dependencies using pip
+You can install/update Datamint and its dependencies using pip
 
 ```bash
-pip install git+https://github.com/SonanceAI/datamint-python-api
+pip install -U datamint
 ```
 
-Soon we will be releasing the package on PyPi.
 We recommend that you install Datamint in a dedicated virtual environment, to avoid conflicting with your system packages.
 Create the enviroment once with `python3 -m venv datamint-env` and then activate it whenever you need it with:
 - `source datamint-env/bin/activate` (Linux/MAC)
@@ -51,7 +50,7 @@ os.environ["DATAMINT_API_KEY"] = "my_api_key"
 Specify API key in the |APIHandlerClass| constructor:
 
 ```python
-from datamintapi import APIHandler
+from datamint import APIHandler
 api = APIHandler(api_key='my_api_key')
 ```
 

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/__init__.py

@@ -1,6 +1,7 @@
 """
-Datamint API is a Python package that provides a simple interface to the Datamint API.
+Datamint API package alias.
 """
+
 import importlib.metadata
 from typing import TYPE_CHECKING
 if TYPE_CHECKING:
@@ -21,5 +22,5 @@ else:
         },
     )
 
-__name__ = "datamintapi"
-__version__ = importlib.metadata.version('datamint')
+__name__ = "datamint"
+__version__ = importlib.metadata.version(__name__)

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/apihandler/annotation_api_handler.py

@@ -541,7 +541,7 @@ class AnnotationAPIHandler(BaseAPIHandler):
 
         Args:
             resource_id (Optional[str]): The resource unique id.
-            annotation_type (Optional[str]): The annotation type. See :class:`~datamintapi.dto.annotation_dto.AnnotationType`.
+            annotation_type (Optional[str]): The annotation type. See :class:`~datamint.dto.annotation_dto.AnnotationType`.
             annotator_email (Optional[str]): The annotator email.
             date_from (Optional[date]): The start date.
             date_to (Optional[date]): The end date.

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/apihandler/api_handler.py

@@ -9,7 +9,7 @@ class APIHandler(RootAPIHandler, ExperimentAPIHandler, AnnotationAPIHandler):
 
     .. code-block:: python
     
-        from datamintapi import APIHandler
+        from datamint import APIHandler
         api = APIHandler()
     """
     pass

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/apihandler/base_api_handler.py

@@ -13,7 +13,7 @@ from io import BytesIO
 import cv2
 import nibabel as nib
 from nibabel.filebasedimages import FileBasedImage as nib_FileBasedImage
-from datamintapi import configs
+from datamint import configs
 from functools import wraps
 
 _LOGGER = logging.getLogger(__name__)

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/apihandler/dto/annotation_dto.py

@@ -18,7 +18,7 @@ import json
 from typing import Any, TypeAlias, Literal
 import logging
 from enum import Enum
-from datamintapi.utils.dicom_utils import pixel_to_patient
+from datamint.utils.dicom_utils import pixel_to_patient
 import pydicom
 import numpy as np
 

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/apihandler/exp_api_handler.py

@@ -1,4 +1,4 @@
-from datamintapi.apihandler.base_api_handler import BaseAPIHandler
+from datamint.apihandler.base_api_handler import BaseAPIHandler
 from typing import Optional, Dict, List, Union, Any
 import json
 import logging

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/apihandler/root_api_handler.py

@@ -6,8 +6,8 @@ from requests.exceptions import HTTPError
 import logging
 import asyncio
 import aiohttp
-from datamintapi.utils.dicom_utils import anonymize_dicom, to_bytesio, is_dicom
-from datamintapi.utils import dicom_utils
+from datamint.utils.dicom_utils import anonymize_dicom, to_bytesio, is_dicom
+from datamint.utils import dicom_utils
 import pydicom
 from pathlib import Path
 from datetime import date
@@ -15,7 +15,7 @@ import mimetypes
 from PIL import Image
 import cv2
 from nibabel.filebasedimages import FileBasedImage as nib_FileBasedImage
-from datamintapi import configs
+from datamint import configs
 from .base_api_handler import BaseAPIHandler, DatamintException, ResourceNotFoundError, ResourceFields, ResourceStatus
 from deprecated.sphinx import deprecated
 import json

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/client_cmd_tools/datamint_config.py

@@ -1,7 +1,7 @@
 import argparse
 import logging
-from datamintapi import configs
-from datamintapi.utils.logging_utils import load_cmdline_logging_config
+from datamint import configs
+from datamint.utils.logging_utils import load_cmdline_logging_config
 
 # Create two loggings: one for the user and one for the developer
 _LOGGER = logging.getLogger(__name__)
@@ -79,7 +79,7 @@ def configure_api_key():
 def test_connection():
     """Test the API connection with current settings."""
     try:
-        from datamintapi import APIHandler
+        from datamint import APIHandler
         _USER_LOGGER.info("🔄 Testing connection...")
         api = APIHandler()
         # Simple test - try to get projects

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/client_cmd_tools/datamint_upload.py

@@ -1,18 +1,18 @@
 import argparse
-from datamintapi.apihandler.api_handler import APIHandler
+from datamint.apihandler.api_handler import APIHandler
 import os
 from humanize import naturalsize
 import logging
 from pathlib import Path
 import sys
-from datamintapi.utils.dicom_utils import is_dicom
+from datamint.utils.dicom_utils import is_dicom
 import fnmatch
 from typing import Sequence, Generator, Optional, Any
 from collections import defaultdict
-from datamintapi import __version__ as datamintapi_version
-from datamintapi import configs
-from datamintapi.client_cmd_tools.datamint_config import ask_api_key
-from datamintapi.utils.logging_utils import load_cmdline_logging_config
+from datamint import __version__ as datamint_version
+from datamint import configs
+from datamint.client_cmd_tools.datamint_config import ask_api_key
+from datamint.utils.logging_utils import load_cmdline_logging_config
 import yaml
 
 # Create two loggings: one for the user and one for the developer
@@ -302,7 +302,7 @@ def _parse_args() -> tuple[Any, list, Optional[list[dict]]]:
                         help='Automatically answer yes to all prompts')
     parser.add_argument('--transpose-segmentation', action='store_true', default=False,
                         help='Transpose the segmentation dimensions to match the image dimensions')
-    parser.add_argument('--version', action='version', version=f'%(prog)s {datamintapi_version}')
+    parser.add_argument('--version', action='version', version=f'%(prog)s {datamint_version}')
     parser.add_argument('--verbose', action='store_true', help='Print debug messages', default=False)
     args = parser.parse_args()
     if args.verbose:

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/dataset/base_dataset.py

@@ -8,13 +8,13 @@ import json
 import yaml
 import pydicom
 import numpy as np
-from datamintapi import configs
+from datamint import configs
 from torch.utils.data import DataLoader
 import torch
-from datamintapi.apihandler.base_api_handler import DatamintException
-from datamintapi.utils.dicom_utils import is_dicom
+from datamint.apihandler.base_api_handler import DatamintException
+from datamint.utils.dicom_utils import is_dicom
 import cv2
-from datamintapi.utils.io_utils import read_array_normalized
+from datamint.utils.io_utils import read_array_normalized
 from deprecated import deprecated
 from datetime import datetime
 
@@ -79,7 +79,7 @@ class DatamintBaseDataset:
                  include_frame_label_names: Optional[list[str]] = None,
                  exclude_frame_label_names: Optional[list[str]] = None
                  ):
-        from datamintapi.apihandler.api_handler import APIHandler
+        from datamint.apihandler.api_handler import APIHandler
         
         if project_name is None:
             raise ValueError("project_name is required.")

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/dataset/dataset.py

@@ -17,7 +17,7 @@ class DatamintDataset(DatamintBaseDataset):
     In addition to that, it has functionality to better process annotations and segmentations.
 
     .. note:: 
-        Import using ``from datamintapi import Dataset``.
+        Import using ``from datamint import Dataset``.
 
     Args:
         root: Root directory of dataset where data already exists or will be downloaded.

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/examples/example_projects.py

@@ -1,6 +1,6 @@
 import requests
 import io
-from datamintapi import APIHandler
+from datamint import APIHandler
 import logging
 from PIL import Image
 import numpy as np

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/experiment/_patcher.py

@@ -486,7 +486,7 @@ def initialize_automatic_logging(enable_rich_logging: bool = True):
     # check if RichHandler is already in the handlers
     if enable_rich_logging and not any(isinstance(h, RichHandler) for h in logging.getLogger().handlers):
         logging.getLogger().handlers.append(RichHandler())  # set rich logging handler for the root logger
-    # logging.getLogger("datamintapi").setLevel(logging.INFO)
+    # logging.getLogger("datamint").setLevel(logging.INFO)
 
     pytorch_patcher = PytorchPatcher()
 

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/experiment/experiment.py

@@ -1,14 +1,14 @@
 import logging
-from datamintapi.apihandler.api_handler import APIHandler
-from datamintapi.apihandler.base_api_handler import DatamintException
+from datamint.apihandler.api_handler import APIHandler
+from datamint.apihandler.base_api_handler import DatamintException
 from datetime import datetime, timezone
 from typing import List, Dict, Optional, Union, Any, Tuple, IO, Literal
 from collections import defaultdict
-from datamintapi.dataset.dataset import DatamintDataset
+from datamint.dataset.dataset import DatamintDataset
 import os
 import numpy as np
 import heapq
-from datamintapi.utils import io_utils
+from datamint.utils import io_utils
 
 _LOGGER = logging.getLogger(__name__)
 
@@ -570,7 +570,7 @@ class Experiment:
 
         Args:
             split (str): The split of the dataset to get. Can be one of ['all', 'train', 'test', 'val'].
-            **kwargs: Additional arguments to pass to the :py:class:`~datamintapi.dataset.dataset.DatamintDataset` class.
+            **kwargs: Additional arguments to pass to the :py:class:`~datamint.dataset.dataset.DatamintDataset` class.
 
         Returns:
             DatamintDataset: The dataset object.
@@ -815,22 +815,22 @@ class Experiment:
         Example:
             .. code-block:: python
 
-            resource_id = '123'
-            predictions = np.array([[0.1, 0.4], [0.9, 0.2]])
-            label_name = 'fracture'
-            exp.log_segmentation_predictions(resource_id, predictions, label_name, threshold=0.5)
+                resource_id = '123'
+                predictions = np.array([[0.1, 0.4], [0.9, 0.2]])
+                label_name = 'fracture'
+                exp.log_segmentation_predictions(resource_id, predictions, label_name, threshold=0.5)
 
             .. code-block:: python
 
-            resource_id = '456'
-            predictions = np.array([[0, 1, 2], [1, 2, 0]])  # Multi-class mask with values 0, 1, 2
-            label_name = {1: 'Femur', 2: 'Tibia'}  # Mapping of pixel values to class names
-            exp.log_segmentation_predictions(
-                resource_id, 
-                predictions, 
-                label_name, 
-                predictions_format='multi-class'
-            )
+                resource_id = '456'
+                predictions = np.array([[0, 1, 2], [1, 2, 0]])  # Multi-class mask with values 0, 1, 2
+                label_name = {1: 'Femur', 2: 'Tibia'}  # Mapping of pixel values to class names
+                exp.log_segmentation_predictions(
+                    resource_id, 
+                    predictions, 
+                    label_name, 
+                    predictions_format='multi-class'
+                )
         """
 
         if predictions_format not in ['multi-class', 'probability']:

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/logging.yaml

@@ -7,13 +7,13 @@ handlers:
     level: WARNING
     show_time: False
   console_user:
-    class: datamintapi.utils.logging_utils.ConditionalRichHandler
+    class: datamint.utils.logging_utils.ConditionalRichHandler
     level: INFO
     show_path: False
     show_time: False
 
 loggers:
-  datamintapi:
+  datamint:
     level: ERROR
     handlers: [console]
     propagate: no

{datamint-1.2.4/datamintapi → datamint-1.3.0/datamint}/utils/logging_utils.py

@@ -45,7 +45,7 @@ def load_cmdline_logging_config():
             with open('logging_dev.yaml', 'r') as f:
                 config = yaml.safe_load(f)
         except:
-            with importlib.resources.open_text('datamintapi', 'logging.yaml') as f:
+            with importlib.resources.open_text('datamint', 'logging.yaml') as f:
                 config = yaml.safe_load(f.read())
 
         logging.config.dictConfig(config)

{datamint-1.2.4 → datamint-1.3.0}/pyproject.toml

@@ -1,19 +1,19 @@
 [project]
 name = "datamint"
 description = "A library for interacting with the Datamint API, designed for efficient data management, processing and Deep Learning workflows."
-version = "1.2.4"
+version = "1.3.0"
 dynamic = ["dependencies"]
 requires-python = ">=3.10"
 readme = "README.md"
 
 [project.scripts]
-datamint-upload = 'datamintapi.client_cmd_tools.datamint_upload:main'
-datamint-config = 'datamintapi.client_cmd_tools.datamint_config:main'
+datamint-upload = 'datamint.client_cmd_tools.datamint_upload:main'
+datamint-config = 'datamint.client_cmd_tools.datamint_config:main'
 
 [tool.poetry]
 # license = "Proprietary" # https://python-poetry.org/docs/pyproject/
-include = [{ path = "datamintapi/logging.yaml", format = ["sdist", "wheel"] }]
-packages = [ { include = "datamint" }, { include = "datamintapi" }]
+include = [{ path = "datamint/logging.yaml", format = ["sdist", "wheel"] }]
+packages = [ { include = "datamint" }]
 
 # https://python-poetry.org/docs/dependency-specification/
 [tool.poetry.dependencies]
@@ -40,6 +40,8 @@ matplotlib = "*"
 lightning = "*"
 albumentations = ">=2.0.0"
 lazy-loader = ">=0.3.0"
+# For compatibility with the datamintapi package
+datamintapi = "0.0.*"
 # Extra dependencies for docs
 sphinx = { version = ">=5.0", optional = true }
 sphinx_rtd_theme = { version = ">=2.0.0", optional = true }

datamint-1.2.4/datamint/__init__.py

@@ -1,11 +0,0 @@
-"""
-Datamint API package alias.
-
-This module serves as an alias for the datamintapi package.
-"""
-
-from datamintapi import *
-import importlib.metadata
-
-__name__ = "datamint"
-__version__ = importlib.metadata.version(__name__)