aignostics 0.2.231__tar.gz → 0.2.233__tar.gz

{aignostics-0.2.231 → aignostics-0.2.233}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.231
+Version: 0.2.233
 Summary: 🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
 Project-URL: Homepage, https://aignostics.readthedocs.io/en/latest/
 Project-URL: Documentation, https://aignostics.readthedocs.io/en/latest/
@@ -49,6 +49,7 @@ Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Classifier: Typing :: Typed
 Requires-Python: <3.15,>=3.11
+Requires-Dist: aiohttp>=3.12.14
 Requires-Dist: boto3<2,>=1.42.4
 Requires-Dist: certifi>=2025.11.12
 Requires-Dist: crc32c<3,>=2.8
@@ -59,7 +60,8 @@ Requires-Dist: duckdb<=2,>=1.4.2
 Requires-Dist: fastapi[all,standard]>=0.123.10
 Requires-Dist: fastparquet>=2024.11.0; python_version < '3.14'
 Requires-Dist: google-cloud-storage<4,>=3.6.0
-Requires-Dist: highdicom<1,>=0.26.1
+Requires-Dist: h11>=0.16.0
+Requires-Dist: highdicom<1,>=0.26.1; python_version < '3.14'
 Requires-Dist: html-sanitizer<3,>=2.6.0
 Requires-Dist: httpx<1,>=0.28.1
 Requires-Dist: humanize<5,>=4.14.0
@@ -68,11 +70,13 @@ Requires-Dist: ijson<4,>=3.4.0.post0
 Requires-Dist: jsf<1,>=0.11.2
 Requires-Dist: jsonschema[format-nongpl]<5,>=4.25.1
 Requires-Dist: loguru<1,>=0.7.3
+Requires-Dist: lxml>=6.0.2
 Requires-Dist: nicegui[native]<4,>=3.4.0
 Requires-Dist: openslide-bin<5,>=4.0.0.10
 Requires-Dist: openslide-python<2,>=1.4.3
 Requires-Dist: packaging<26,>=25.0
 Requires-Dist: pandas<3,>=2.3.3
+Requires-Dist: pillow>=11.3.0
 Requires-Dist: platformdirs<5,>=4.3.2
 Requires-Dist: platformdirs<5,>=4.5.1
 Requires-Dist: procrastinate>=3.5.3
@@ -85,23 +89,30 @@ Requires-Dist: pywin32<312,>=311; sys_platform == 'win32'
 Requires-Dist: pyyaml<7,>=6.0.3
 Requires-Dist: requests-oauthlib<3,>=2.0.0
 Requires-Dist: requests<3,>=2.32.5
+Requires-Dist: rfc3987; sys_platform == 'never'
 Requires-Dist: s5cmd<1,>=0.3.3
 Requires-Dist: semver<4,>=3.0.4
 Requires-Dist: sentry-sdk<3,>=2.47.0
 Requires-Dist: shapely<3,>=2.1.2
+Requires-Dist: starlette>=0.47.2
+Requires-Dist: starlette>=0.49.1
 Requires-Dist: tenacity<10,>=9.1.2
+Requires-Dist: tornado>=6.5.0
 Requires-Dist: tqdm<5,>=4.67.1
 Requires-Dist: truststore<1,>=0.10.4
 Requires-Dist: typer<1,>=0.20.0
 Requires-Dist: uptime<4,>=3.0.1
 Requires-Dist: urllib3<3,>=2.6.1
+Requires-Dist: urllib3>=2.5.0
 Requires-Dist: wsidicom<1,>=0.28.1
 Provides-Extra: jupyter
+Requires-Dist: jupyter-core>=5.8.1; extra == 'jupyter'
 Requires-Dist: jupyter<2,>=1.1.1; extra == 'jupyter'
+Requires-Dist: jupyterlab>=4.4.9; extra == 'jupyter'
 Provides-Extra: marimo
 Requires-Dist: cloudpathlib<1,>=0.23.0; extra == 'marimo'
 Requires-Dist: ipython<10,>=9.8.0; extra == 'marimo'
-Requires-Dist: marimo<1,>=0.18.3; extra == 'marimo'
+Requires-Dist: marimo<1,>=0.18.4; extra == 'marimo'
 Requires-Dist: matplotlib<4,>=3.10.7; extra == 'marimo'
 Requires-Dist: shapely<3,>=2.1.0; extra == 'marimo'
 Provides-Extra: pyinstaller

{aignostics-0.2.231 → aignostics-0.2.233}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.231",
+#     "aignostics==0.2.233",
 # ]
 # ///
 

{aignostics-0.2.231 → aignostics-0.2.233}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.231"
+version = "0.2.233"
 description = "🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library."
 readme = "README.md"
 authors = [
@@ -71,6 +71,7 @@ classifiers = [
     "Natural Language :: English",
 ]
 
+# WARNING: The upper bound of requires-python is *not* respected by uvx
 requires-python = ">=3.11, <3.15"
 
 dependencies = [
@@ -96,7 +97,7 @@ dependencies = [
     "duckdb>=1.4.2,<=2",
     "google-cloud-storage>=3.6.0,<4",
     "crc32c>=2.8,<3", # TODO(Helmut): Remove and back to google_crc32c when that supports Python 3.14
-    "highdicom>=0.26.1,<1",
+    "highdicom>=0.26.1,<1; python_version < '3.14'", # transitive dependency pyjpegls not yet supporting Python 3.14
     "html-sanitizer>=2.6.0,<3",
     "httpx>=0.28.1,<1",
     "idc-index-data==23.0.1",
@@ -124,15 +125,32 @@ dependencies = [
     "truststore>=0.10.4,<1",
     "urllib3>=2.6.1,<3",
     "wsidicom>=0.28.1,<1",
+    # Transitive overrides
+    # WARNING: one cannot negate or downgrade a dependency required here. use override-dependencies for that.
+    "rfc3987; sys_platform == 'never'", # GPLv3
+    "h11>=0.16.0",                      # CVE-2025-43859
+    "tornado>=6.5.0",                   # CVE-2025-47287
+    "urllib3>=2.5.0",                   # CVE-2025-50181, CVE-2025-50182,
+    "pillow>=11.3.0",                   # CVE-2025-48379,
+    "aiohttp>=3.12.14",                 # CVE-2025-53643
+    "starlette>=0.47.2",                # CVE-2025-54121
+    "starlette>=0.49.1",                # GHSA-7f5h-v6xp-fcq8
+    "lxml>=6.0.2",                      # For python 3.14 pre-built wheels
 ]
 
 [project.optional-dependencies]
 pyinstaller = ["pyinstaller>=6.14.0,<7"]
-jupyter = ["jupyter>=1.1.1,<2"]
+jupyter = [
+    "jupyter>=1.1.1,<2",    
+    # Transitive overrides
+    # WARNING: one cannot negate or downgrade a dependency required here. use override-dependencies for that.
+    "jupyter-core>=5.8.1",              # CVE-2025-30167
+    "jupyterlab>=4.4.9",                # CVE-2025-59842
+]
 marimo = [
     "cloudpathlib>=0.23.0,<1",
     "ipython>=9.8.0,<10",
-    "marimo>=0.18.3,<1",
+    "marimo>=0.18.4,<1",
     "matplotlib>=3.10.7,<4",
     "shapely>=2.1.0,<3",
 ]
@@ -185,27 +203,18 @@ dev = [
     "types-pyyaml>=6.0.12.20250915,<7",
     "types-requests>=2.32.4.20250913,<3",
     "watchdog>=6.0.0,<7",
+    # Transitive overrides
+    # WARNING: one cannot negate or downgrade a dependency required here. use override-dependencies for that.
+    "pip>=5.3",                         # CVE-2025-8869  
+    "uv>=0.9.7",                        # CVE-2025-54368, GHSA-w476-p2h3-79g9, GHSA-pqhf-p39g-3x64
+    "fonttools>=4.60.2",                # CVE-2025-66034 (GHSA-768j-98cg-p3fv), dep of matplotlib
 ]
 
 [tool.uv]
 required-version = ">=0.9.7" # CVE-2025-54368, GHSA-w476-p2h3-79g9, GHSA-pqhf-p39g-3x64
+# WARNING: override-dependencies is *not* respected by uvx
 override-dependencies = [ # https://github.com/astral-sh/uv/issues/4422
-    "rfc3987; sys_platform == 'never'", # GPLv3
-    "h11>=0.16.0",                      # CVE-2025-43859
-    "tornado>=6.5.0",                   # CVE-2025-47287
-    "jupyter-core>=5.8.1",              # CVE-2025-30167
-    "urllib3>=2.5.0",                   # CVE-2025-50181, CVE-2025-50182,
-    "pillow>=11.3.0",                   # CVE-2025-48379,
-    "aiohttp>=3.12.14",                 # CVE-2025-53643
-    "starlette>=0.47.2",                # CVE-2025-54121
-    "uv>=0.9.7",                        # CVE-2025-54368, GHSA-w476-p2h3-79g9, GHSA-pqhf-p39g-3x64
-    "jupyterlab>=4.4.9",                # CVE-2025-59842
-    "pip>=5.3",                         # CVE-2025-8869  
-    "starlette>=0.49.1",                # GHSA-7f5h-v6xp-fcq8
-    "fonttools>=4.60.2",                # CVE-2025-66034 (GHSA-768j-98cg-p3fv), dep of matplotlib
-    "pyjpegls; python_version < '3.14'", # No Python 3.14 support yet
-    "pytest>=9.0.1",                    # pytest-md-report depends on pytest<9 unnecessarily
-    "lxml>=6.0.2",                      # For python 3.14 pre-built wheels
+    "pytest>=9.0.1",    # pytest-md-report depends on pytest<9 unnecessarily
 ]
 
 [tool.uv.sources]
@@ -386,7 +395,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.231"
+current_version = "0.2.233"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.231 → aignostics-0.2.233}/src/aignostics/qupath/_service.py

@@ -42,6 +42,7 @@ QUPATH_SCRIPT_MAX_EXECUTION_TIME = 60 * 60 * 2  # seconds, maximum wait time for
 
 PROJECT_FILENAME = "project.qpproj"
 ANNOTATIONS_BATCH_SIZE = 500000
+JSON_SUFFIX = ".json"
 
 
 class QuPathVersion(BaseModel):
@@ -1124,40 +1125,46 @@ class Service(BaseService):
             progress_callable(progress)
 
         # We communicate via file I/O with the Groovy script running within QuPath
-        with (
-            tempfile.NamedTemporaryFile(mode="w", suffix=".json", encoding="utf-8") as paths_file,
-            tempfile.NamedTemporaryFile(mode="w", suffix=".json", encoding="utf-8") as output_file,
-        ):
-            try:
-                json.dump([str(path.resolve()) for path in paths], paths_file.file)
-                paths_file.flush()
+        # Use delete=False to avoid Windows file locking issues - the file must be closed
+        # before QuPath can read it, but NamedTemporaryFile keeps files locked while open on Windows
+        paths_file = tempfile.NamedTemporaryFile(mode="w", suffix=JSON_SUFFIX, encoding="utf-8", delete=False)  # noqa: SIM115
+        output_file = tempfile.NamedTemporaryFile(mode="w", suffix=JSON_SUFFIX, encoding="utf-8", delete=False)  # noqa: SIM115
+        try:
+            # Write paths and close file so QuPath can read it
+            json.dump([str(path.resolve()) for path in paths], paths_file)
+            paths_file.close()
+            output_file.close()
 
-                pid = Service.execute_qupath(
-                    script=Service._find_groovy_script("add"),
-                    script_args=[str(project), str(paths_file.name), str(output_file.name)],
-                )
+            pid = Service.execute_qupath(
+                script=Service._find_groovy_script("add"),
+                script_args=[str(project), paths_file.name, output_file.name],
+            )
 
-                if not pid:
-                    message = "Failed to execute QuPath script for adding images."
-                    logger.error(message)
-                    raise RuntimeError(message)  # noqa: TRY301
-
-                with Path(output_file.name).open("r", encoding="utf-8") as f:
-                    result_data = json.load(f)
-                added_count = int(result_data.get("added_count", 0))
-                errors = result_data.get("errors", [])
-                for error in errors:
-                    logger.warning(f"QuPath add script error: {error}")
-
-                if progress_callable:
-                    progress.status = AddProgressState.COMPLETED
-                    progress_callable(progress)
-
-                return added_count
-            except Exception as e:
-                message = f"Failed to add images to QuPath project: {e!s}"
-                logger.exception(message)
-                raise RuntimeError(message) from e
+            if not pid:
+                message = "Failed to execute QuPath script for adding images."
+                logger.error(message)
+                raise RuntimeError(message)  # noqa: TRY301
+
+            with Path(output_file.name).open("r", encoding="utf-8") as f:
+                result_data = json.load(f)
+            added_count = int(result_data.get("added_count", 0))
+            errors = result_data.get("errors", [])
+            for error in errors:
+                logger.warning(f"QuPath add script error: {error}")
+
+            if progress_callable:
+                progress.status = AddProgressState.COMPLETED
+                progress_callable(progress)
+
+            return added_count
+        except Exception as e:
+            message = f"Failed to add images to QuPath project: {e!s}"
+            logger.exception(message)
+            raise RuntimeError(message) from e
+        finally:
+            # Clean up temp files
+            Path(paths_file.name).unlink(missing_ok=True)
+            Path(output_file.name).unlink(missing_ok=True)
 
     @staticmethod
     def annotate(
@@ -1246,9 +1253,12 @@ class Service(BaseService):
             RuntimeError: If there is an error inspecting the project.
         """
         # We communicate via file I/O with the Groovy script running within QuPath
-        with tempfile.NamedTemporaryFile(mode="w+", suffix=".json", encoding="utf-8") as temp_file:
-            output_file = Path(temp_file.name).resolve()
-
+        # Use delete=False to avoid Windows file locking issues - the file must be closed
+        # before QuPath can write to it, but NamedTemporaryFile keeps files locked while open on Windows
+        temp_file = tempfile.NamedTemporaryFile(mode="w+", suffix=JSON_SUFFIX, encoding="utf-8", delete=False)  # noqa: SIM115
+        output_file = Path(temp_file.name).resolve()
+        temp_file.close()
+        try:
             pid = Service.execute_qupath(
                 quiet=True,
                 project=project,
@@ -1267,3 +1277,5 @@ class Service(BaseService):
                 raise RuntimeError(message)
 
             return QuPathProject.model_validate_json(output_file.read_text(encoding="utf-8"))
+        finally:
+            output_file.unlink(missing_ok=True)

{aignostics-0.2.231 → aignostics-0.2.233}/src/aignostics/utils/__init__.py

@@ -22,7 +22,7 @@ from ._constants import (
     __version__,
     __version_full__,
 )
-from ._di import load_modules, locate_implementations, locate_subclasses
+from ._di import discover_plugin_packages, load_modules, locate_implementations, locate_subclasses
 from ._fs import get_user_data_directory, open_user_data_directory, sanitize_path, sanitize_path_component
 from ._health import Health
 from ._log import LogSettings
@@ -60,6 +60,7 @@ __all__ = [
     "__version_full__",
     "boot",
     "console",
+    "discover_plugin_packages",
     "get_process_info",
     "get_user_data_directory",
     "load_modules",

aignostics-0.2.233/src/aignostics/utils/_di.py

@@ -0,0 +1,113 @@
+"""Module for dynamic import and discovery of implementations and subclasses."""
+
+import importlib
+import pkgutil
+from functools import lru_cache
+from importlib.metadata import entry_points
+from inspect import isclass
+from typing import Any
+
+from ._constants import __project_name__
+
+_implementation_cache: dict[Any, list[Any]] = {}
+_subclass_cache: dict[Any, list[Any]] = {}
+
+# Entry point group name for aignostics plugins
+PLUGIN_ENTRY_POINT_GROUP = "aignostics.plugins"
+
+
+@lru_cache(maxsize=1)
+def discover_plugin_packages() -> tuple[str, ...]:
+    """
+    Discover plugin packages using entry points.
+
+    Plugins register themselves in their pyproject.toml:
+
+        [project.entry-points."aignostics.plugins"]
+        my_plugin = "my_plugin"
+
+    Results are cached after the first call.
+
+    Returns:
+        tuple[str, ...]: Tuple of discovered plugin package names.
+    """
+    eps = entry_points(group=PLUGIN_ENTRY_POINT_GROUP)
+    return tuple(ep.value for ep in eps)
+
+
+def load_modules() -> None:
+    package = importlib.import_module(__project_name__)
+    for _, name, _ in pkgutil.iter_modules(package.__path__):
+        importlib.import_module(f"{__project_name__}.{name}")
+
+
+def locate_implementations(_class: type[Any]) -> list[Any]:
+    """
+    Dynamically discover all instances of some class.
+
+    Searches in the main project and all plugins registered via entry points.
+
+    Args:
+        _class (type[Any]): Class to search for.
+
+    Returns:
+        list[Any]: List of discovered implementations of the given class.
+    """
+    if _class in _implementation_cache:
+        return _implementation_cache[_class]
+
+    plugin_packages = discover_plugin_packages()
+
+    implementations = []
+    for package_name in [*plugin_packages, __project_name__]:
+        package = importlib.import_module(package_name)
+
+        for _, name, _ in pkgutil.iter_modules(package.__path__):
+            module = importlib.import_module(f"{package_name}.{name}")
+            # Check all members of the module
+            for member_name in dir(module):
+                member = getattr(module, member_name)
+                if isinstance(member, _class):
+                    implementations.append(member)
+
+    _implementation_cache[_class] = implementations
+    return implementations
+
+
+def locate_subclasses(_class: type[Any]) -> list[Any]:
+    """
+    Dynamically discover all classes that are subclasses of some type.
+
+    Searches in the main project and all plugins registered via entry points.
+
+    Args:
+        _class (type[Any]): Parent class of subclasses to search for.
+
+    Returns:
+        list[type[Any]]: List of discovered subclasses of the given class.
+    """
+    if _class in _subclass_cache:
+        return _subclass_cache[_class]
+
+    plugin_packages = discover_plugin_packages()
+
+    subclasses = []
+    for package_name in [*plugin_packages, __project_name__]:
+        try:
+            package = importlib.import_module(package_name)
+        except ImportError:
+            continue
+
+        for _, name, _ in pkgutil.iter_modules(package.__path__):
+            try:
+                module = importlib.import_module(f"{package_name}.{name}")
+                # Check all members of the module
+                for member_name in dir(module):
+                    member = getattr(module, member_name)
+                    if isclass(member) and issubclass(member, _class) and member != _class:
+                        subclasses.append(member)
+            except ImportError:
+                continue
+
+    _subclass_cache[_class] = subclasses
+    return subclasses

{aignostics-0.2.231 → aignostics-0.2.233}/src/aignostics/utils/_gui.py

@@ -73,6 +73,12 @@ def gui_run(  # noqa: PLR0913, PLR0917
         native = False
         show = True
 
+    # On Windows with python 3.14 don't use native mode due to pythonnet not yet
+    # supported
+    if native and platform.system() == "Windows" and platform.python_version_tuple() >= ("3", "14"):
+        native = False
+        show = True
+
     gui_register_pages()
 
     ui.run(

{aignostics-0.2.231 → aignostics-0.2.233}/src/aignostics/wsi/_cli.py

@@ -12,6 +12,33 @@ from aignostics.utils import console
 from ._service import Service
 from ._utils import print_slide_info, print_study_info
 
+# Python version for highdicom compatibility check
+_PYTHON_VERSION = f"{sys.version_info.major}.{sys.version_info.minor}"
+_HIGHDICOM_UNSUPPORTED_VERSIONS = {"3.14"}
+
+
+def _check_highdicom_available() -> bool:
+    """Check if highdicom is available (not supported on Python 3.14+).
+
+    Returns:
+        True if highdicom can be imported, False otherwise.
+    """
+    try:
+        from ._pydicom_handler import PydicomHandler  # noqa: PLC0415, F401
+
+        return True
+    except ImportError:
+        return False
+
+
+def _print_highdicom_unsupported_error() -> None:
+    """Print error message when highdicom is not available."""
+    console.print(f"[red]This command requires 'highdicom' which is not available on Python {_PYTHON_VERSION}.[/red]")
+    console.print("[yellow]Please run with Python 3.13 or earlier:[/yellow]")
+    console.print("[green]  uvx -p 3.13 aignostics wsi dicom <command> ...[/green]")
+    sys.exit(1)
+
+
 cli = typer.Typer(name="wsi", help="Operations on whole slide images.")
 
 
@@ -107,6 +134,10 @@ def dicom_inspect(
     summary: Annotated[bool, typer.Option(help="Show only summary information")] = False,
 ) -> None:  # pylint: disable=W0613
     """Inspect DICOM files at any hierarchy level."""
+    if not _check_highdicom_available():
+        _print_highdicom_unsupported_error()
+        return
+
     from ._pydicom_handler import PydicomHandler  # noqa: PLC0415
 
     try:
@@ -139,6 +170,10 @@ def dicom_geojson_import(
     geojson_path: Annotated[Path, typer.Argument(help="Path to the GeoJSON file", exists=True)],
 ) -> None:  # pylint: disable=W0613
     """Import GeoJSON annotations into DICOM ANN instance."""
+    if not _check_highdicom_available():
+        _print_highdicom_unsupported_error()
+        return
+
     from ._pydicom_handler import PydicomHandler  # noqa: PLC0415
 
     try:

aignostics-0.2.231/src/aignostics/utils/_di.py

@@ -1,76 +0,0 @@
-"""Module for dynamic import and discovery of implementations and subclasses."""
-
-import importlib
-import pkgutil
-from inspect import isclass
-from typing import Any
-
-from ._constants import __project_name__
-
-_implementation_cache: dict[Any, list[Any]] = {}
-_subclass_cache: dict[Any, list[Any]] = {}
-
-
-def load_modules() -> None:
-    package = importlib.import_module(__project_name__)
-    for _, name, _ in pkgutil.iter_modules(package.__path__):
-        importlib.import_module(f"{__project_name__}.{name}")
-
-
-def locate_implementations(_class: type[Any]) -> list[Any]:
-    """
-    Dynamically discover all instances of some class.
-
-    Args:
-        _class (type[Any]): Class to search for.
-
-    Returns:
-        list[Any]: List of discovered implementations of the given class.
-    """
-    if _class in _implementation_cache:
-        return _implementation_cache[_class]
-
-    implementations = []
-    package = importlib.import_module(__project_name__)
-
-    for _, name, _ in pkgutil.iter_modules(package.__path__):
-        module = importlib.import_module(f"{__project_name__}.{name}")
-        # Check all members of the module
-        for member_name in dir(module):
-            member = getattr(module, member_name)
-            if isinstance(member, _class):
-                implementations.append(member)
-
-    _implementation_cache[_class] = implementations
-    return implementations
-
-
-def locate_subclasses(_class: type[Any]) -> list[Any]:
-    """
-    Dynamically discover all classes that are subclasses of some type.
-
-    Args:
-        _class (type[Any]): Parent class of subclasses to search for.
-
-    Returns:
-        list[type[Any]]: List of discovered subclasses of the given class.
-    """
-    if _class in _subclass_cache:
-        return _subclass_cache[_class]
-
-    subclasses = []
-    package = importlib.import_module(__project_name__)
-
-    for _, name, _ in pkgutil.iter_modules(package.__path__):
-        try:
-            module = importlib.import_module(f"{__project_name__}.{name}")
-            # Check all members of the module
-            for member_name in dir(module):
-                member = getattr(module, member_name)
-                if isclass(member) and issubclass(member, _class) and member != _class:
-                    subclasses.append(member)
-        except ImportError:
-            continue
-
-    _subclass_cache[_class] = subclasses
-    return subclasses