aignostics 0.2.147__tar.gz → 0.2.153__tar.gz

{aignostics-0.2.147 → aignostics-0.2.153}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aignostics
-Version: 0.2.147
+Version: 0.2.153
 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/
@@ -50,7 +50,7 @@ Classifier: Typing :: Typed
 Requires-Python: <4.0,>=3.11
 Requires-Dist: boto3>=1.40.11
 Requires-Dist: certifi>=2025.8.3
-Requires-Dist: dicom-validator>=0.7.1
+Requires-Dist: dicom-validator>=0.7.2
 Requires-Dist: dicomweb-client[gcp]>=0.59.2
 Requires-Dist: duckdb<=1.4.0,>=0.10.0
 Requires-Dist: fastapi[all,standard]>=0.116.1
@@ -63,7 +63,7 @@ Requires-Dist: humanize>=4.12.3
 Requires-Dist: idc-index-data==21.0.0
 Requires-Dist: ijson>=3.4.0
 Requires-Dist: jsf>=0.11.2
-Requires-Dist: jsonschema>=4.24.1
+Requires-Dist: jsonschema[format-nongpl]>=4.24.1
 Requires-Dist: logfire[system-metrics]>=4.3.3
 Requires-Dist: nicegui[native]>=2.22.2
 Requires-Dist: openslide-bin>=4.0.0.8
@@ -93,6 +93,7 @@ Requires-Dist: sentry-sdk>=2.35.0
 Requires-Dist: shapely>=2.1.1
 Requires-Dist: show-in-file-manager>=1.1.5
 Requires-Dist: tqdm>=4.67.1
+Requires-Dist: truststore>=0.10.4
 Requires-Dist: typer>=0.16.0
 Requires-Dist: uptime>=3.0.1
 Requires-Dist: urllib3>=2.5.0

aignostics-0.2.153/dist_native_all/dist_native-windows-latest/extracted/aignostics/_internal/boto3/examples/cloudfront.rst

@@ -0,0 +1,35 @@
+Generate a signed URL for Amazon CloudFront
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following example shows how to generate a signed URL for Amazon CloudFront.
+Note that you will need the ``cryptography`` `library <https://cryptography.io/en/latest/>`__ to follow this example::
+
+    import datetime
+
+    from cryptography.hazmat.backends import default_backend
+    from cryptography.hazmat.primitives import hashes
+    from cryptography.hazmat.primitives import serialization
+    from cryptography.hazmat.primitives.asymmetric import padding
+    from botocore.signers import CloudFrontSigner
+
+
+    def rsa_signer(message):
+        with open('path/to/key.pem', 'rb') as key_file:
+            private_key = serialization.load_pem_private_key(
+                key_file.read(),
+                password=None,
+                backend=default_backend()
+            )
+        return private_key.sign(message, padding.PKCS1v15(), hashes.SHA1())
+
+    key_id = 'AKIAIOSFODNN7EXAMPLE'
+    url = 'http://d2949o5mkkp72v.cloudfront.net/hello.txt'
+    expire_date = datetime.datetime(2017, 1, 1)
+
+    cloudfront_signer = CloudFrontSigner(key_id, rsa_signer)
+
+    # Create a signed url that will be valid until the specific expiry date
+    # provided using a canned policy.
+    signed_url = cloudfront_signer.generate_presigned_url(
+        url, date_less_than=expire_date)
+    print(signed_url)

aignostics-0.2.153/dist_native_all/dist_native-windows-latest/extracted/aignostics/_internal/boto3/examples/s3.rst

@@ -0,0 +1,185 @@
+List objects in an Amazon S3 bucket
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following example shows how to use an Amazon S3 bucket resource to list
+the objects in the bucket.
+
+.. code-block:: python
+
+    import boto3
+
+    s3 = boto3.resource('s3')
+    bucket = s3.Bucket('amzn-s3-demo-bucket')
+    for obj in bucket.objects.all():
+        print(obj.key)
+
+
+List top-level common prefixes in Amazon S3 bucket
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example shows how to list all of the top-level common prefixes in an
+Amazon S3 bucket:
+
+.. code-block:: python
+
+    import boto3
+
+    client = boto3.client('s3')
+    paginator = client.get_paginator('list_objects')
+    result = paginator.paginate(Bucket='amzn-s3-demo-bucket', Delimiter='/')
+    for prefix in result.search('CommonPrefixes'):
+        print(prefix.get('Prefix'))
+
+
+Restore Glacier objects in an Amazon S3 bucket
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following example shows how to initiate restoration of glacier objects in
+an Amazon S3 bucket, determine if a restoration is on-going, and determine if a
+restoration is finished.
+
+.. code-block:: python
+
+    import boto3
+
+    s3 = boto3.resource('s3')
+    bucket = s3.Bucket('amzn-s3-demo-bucket')
+    for obj_sum in bucket.objects.all():
+        obj = s3.Object(obj_sum.bucket_name, obj_sum.key)
+        if obj.storage_class == 'GLACIER':
+            # Try to restore the object if the storage class is glacier and
+            # the object does not have a completed or ongoing restoration
+            # request.
+            if obj.restore is None:
+                print('Submitting restoration request: %s' % obj.key)
+                obj.restore_object(RestoreRequest={'Days': 1})
+            # Print out objects whose restoration is on-going
+            elif 'ongoing-request="true"' in obj.restore:
+                print('Restoration in-progress: %s' % obj.key)
+            # Print out objects whose restoration is complete
+            elif 'ongoing-request="false"' in obj.restore:
+                print('Restoration complete: %s' % obj.key)
+
+
+Uploading/downloading files using SSE KMS
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example shows how to use SSE-KMS to upload objects using
+server side encryption with a key managed by KMS.
+
+We can either use the default KMS master key, or create a
+custom key in AWS and use it to encrypt the object by passing in its
+key id.
+
+With KMS, nothing else needs to be provided for getting the
+object; S3 already knows how to decrypt the object.
+
+
+.. code-block:: python
+
+    import boto3
+    import os
+
+    BUCKET = 'amzn-s3-demo-bucket'
+    s3 = boto3.client('s3')
+    keyid = '<the key id>'
+
+    print("Uploading S3 object with SSE-KMS")
+    s3.put_object(Bucket=BUCKET,
+                  Key='encrypt-key',
+                  Body=b'foobar',
+                  ServerSideEncryption='aws:kms',
+                  # Optional: SSEKMSKeyId
+                  SSEKMSKeyId=keyid)
+    print("Done")
+
+    # Getting the object:
+    print("Getting S3 object...")
+    response = s3.get_object(Bucket=BUCKET,
+                             Key='encrypt-key')
+    print("Done, response body:")
+    print(response['Body'].read())
+
+
+Uploading/downloading files using SSE Customer Keys
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example shows how to use SSE-C to upload objects using
+server side encryption with a customer provided key.
+
+First, we'll need a 32 byte key.  For this example, we'll
+randomly generate a key but you can use any 32 byte key
+you want.  Remember, you must the same key to download
+the object.  If you lose the encryption key, you lose
+the object.
+
+Also note how we don't have to provide the SSECustomerKeyMD5.
+Boto3 will automatically compute this value for us.
+
+
+.. code-block:: python
+
+    import boto3
+    import os
+
+    BUCKET = 'amzn-s3-demo-bucket'
+    KEY = os.urandom(32)
+    s3 = boto3.client('s3')
+
+    print("Uploading S3 object with SSE-C")
+    s3.put_object(Bucket=BUCKET,
+                  Key='encrypt-key',
+                  Body=b'foobar',
+                  SSECustomerKey=KEY,
+                  SSECustomerAlgorithm='AES256')
+    print("Done")
+
+    # Getting the object:
+    print("Getting S3 object...")
+    # Note how we're using the same ``KEY`` we
+    # created earlier.
+    response = s3.get_object(Bucket=BUCKET,
+                             Key='encrypt-key',
+                             SSECustomerKey=KEY,
+                             SSECustomerAlgorithm='AES256')
+    print("Done, response body:")
+    print(response['Body'].read())
+
+
+Downloading a specific version of an S3 object
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example shows how to download a specific version of an
+S3 object.
+
+.. code-block:: python
+
+    import boto3
+    s3 = boto3.client('s3')
+
+    s3.download_file(
+        "amzn-s3-demo-bucket", "key-name", "tmp.txt",
+        ExtraArgs={"VersionId": "my-version-id"}
+    )
+
+
+Filter objects by last modified time using JMESPath
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example shows how to filter objects by last modified time
+using JMESPath.
+
+.. code-block:: python
+
+    import boto3
+    s3 = boto3.client("s3")
+
+    s3_paginator = s3.get_paginator('list_objects_v2')
+    s3_iterator = s3_paginator.paginate(Bucket='amzn-s3-demo-bucket')
+
+    filtered_iterator = s3_iterator.search(
+        "Contents[?to_string(LastModified)>='\"2022-01-05 08:05:37+00:00\"'].Key"
+    )
+
+    for key_data in filtered_iterator:
+        print(key_data)

{aignostics-0.2.147 → aignostics-0.2.153}/examples/notebook.py

@@ -2,7 +2,7 @@
 # requires-python = ">=3.13"
 # dependencies = [
 #     "marimo",
-#     "aignostics==0.2.147",
+#     "aignostics==0.2.153",
 # ]
 # ///
 

{aignostics-0.2.147 → aignostics-0.2.153}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "aignostics"
-version = "0.2.147"
+version = "0.2.153"
 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 = [
@@ -99,7 +99,7 @@ dependencies = [
     "platformdirs>=4.3.8",
     "boto3>=1.40.11",
     "certifi>=2025.8.3",
-    "dicom-validator>=0.7.1",
+    "dicom-validator>=0.7.2",
     "dicomweb-client[gcp]>=0.59.2",
     "duckdb>=0.10.0,<=1.4.0",
     "fastparquet>=2024.11.0",
@@ -110,7 +110,7 @@ dependencies = [
     "idc-index-data==21.0.0",
     "ijson>=3.4.0",
     "jsf>=0.11.2",
-    "jsonschema>=4.24.1",
+    "jsonschema[format-nongpl]>=4.24.1",
     "openslide-bin>=4.0.0.8",
     "openslide-python>=1.4.2",
     "pandas<=2.3.1",
@@ -126,6 +126,7 @@ dependencies = [
     "tqdm>=4.67.1",
     "urllib3>=2.5.0",
     "wsidicom>=0.27.1",
+    "truststore>=0.10.4",
 ]
 
 [project.optional-dependencies]
@@ -358,7 +359,7 @@ source = ["src/"]
 
 
 [tool.bumpversion]
-current_version = "0.2.147"
+current_version = "0.2.153"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"

{aignostics-0.2.147 → aignostics-0.2.153}/src/aignostics/application/_gui/_page_index.py

@@ -1,5 +1,6 @@
 """GUI of application module including homepage of Aignostics Launchpad."""
 
+import platform
 from importlib.util import find_spec
 
 from nicegui import Client, app, ui  # noq
@@ -10,14 +11,28 @@ from ._frame import _frame
 
 logger = get_logger(__name__)
 
+if platform.system() != "Darwin":
+    try:
+        import pyi_splash  # pyright: ignore[reportMissingModuleSource]
+    except ImportError:
+        pyi_splash = None
+else:
+    pyi_splash = None
+
 
 async def _page_index(client: Client) -> None:
     """Homepage of Applications."""
     client.content.classes(remove="nicegui-content")
     client.content.classes(add="pl-5 pt-5")
 
+    if pyi_splash and pyi_splash.is_alive():
+        pyi_splash.update_text("Connecting with API ...")
+
     await _frame("Analyze your Whole Slide Images with AI", left_sidebar=True)
 
+    if pyi_splash and pyi_splash.is_alive():
+        pyi_splash.close()
+
     with ui.row().classes("p-4 pt-2 pr-0"), ui.column():
         await ui.context.client.connected()
         ui.label("Welcome to the Aignostics Launchpad").bind_text_from(

{aignostics-0.2.147 → aignostics-0.2.153}/src/aignostics/system/_service.py

@@ -4,6 +4,7 @@ import json
 import os
 import platform
 import re
+import ssl
 import sys
 import typing as t
 from http import HTTPStatus
@@ -333,6 +334,9 @@ class Service(BaseService):
                         "public_ipv4": Service._get_public_ipv4(),
                         "proxies": getproxies(),
                         "requests_ca_bundle": os.getenv("REQUESTS_CA_BUNDLE"),
+                        "ssl_cert_file": os.getenv("SSL_CERT_FILE"),
+                        "ssl_cert_dir": os.getenv("SSL_CERT_DIR"),
+                        "ssl_default_verify_paths": ssl.get_default_verify_paths()._asdict(),
                     },
                     "uptime": {
                         "seconds": uptime(),

{aignostics-0.2.147 → aignostics-0.2.153}/src/aignostics/utils/boot.py

@@ -6,13 +6,12 @@ import sys
 from pathlib import Path
 
 import certifi
+import truststore
 
 from ._log import logging_initialize
 
 _boot_called = False
 
-if ssl.get_default_verify_paths().cafile is None and os.environ.get("SSL_CERT_FILE") is None:
-    os.environ["SSL_CERT_FILE"] = certifi.where()
 
 # Import third party dependencies
 third_party_dir = Path(__file__).parent.absolute() / ".." / "third_party"
@@ -33,6 +32,11 @@ def boot(modules_to_instrument: list[str]) -> None:
         return
     _boot_called = True
 
+    truststore.inject_into_ssl()
+
+    if ssl.get_default_verify_paths().cafile is None and os.environ.get("SSL_CERT_FILE") is None:
+        os.environ["SSL_CERT_FILE"] = certifi.where()
+
     from ._sentry import sentry_initialize  # noqa: PLC0415
 
     sentry_initialize()

{aignostics-0.2.147 → aignostics-0.2.153}/src/aignostics.py

@@ -1,21 +1,34 @@
 """Aignostics Launchpad launcher for pyinstaller."""
 
 import os
+import platform
 import ssl
 import sys
 from multiprocessing import freeze_support
 
 freeze_support()
 
+if platform.system() != "Darwin":
+    try:
+        import pyi_splash  # pyright: ignore[reportMissingModuleSource]
+    except ImportError:
+        pyi_splash = None
+else:
+    pyi_splash = None
+
+if pyi_splash and pyi_splash.is_alive():
+    pyi_splash.update_text("Initializing services ...")
+
 os.environ["LOGFIRE_PYDANTIC_RECORD"] = "off"
 
 from aignostics.constants import MODULES_TO_INSTRUMENT  # noqa: E402
 from aignostics.utils import boot, get_logger, gui_run  # noqa: E402
 
 boot(MODULES_TO_INSTRUMENT)
+
 logger = get_logger(__name__)
 
-# Constants for command line argument handling
+
 EXEC_SCRIPT_FLAG = "--exec-script"
 MIN_ARGS_FOR_SCRIPT = 3  # program name, flag, and script content
 MODULE_FLAG = "--run-module"
@@ -23,9 +36,7 @@ MIN_ARGS_FOR_MODULE = 3  # program name, flag, and module name
 
 DEBUG_FLAG = "--debug"
 
-# Check if we should execute a script instead of launching the GUI
 if len(sys.argv) > 1 and sys.argv[1] == EXEC_SCRIPT_FLAG:
-    # Execute the script passed as the second argument
     if len(sys.argv) >= MIN_ARGS_FOR_SCRIPT:
         script_content = sys.argv[2]
         try:
@@ -37,23 +48,19 @@ if len(sys.argv) > 1 and sys.argv[1] == EXEC_SCRIPT_FLAG:
         logger.error("No script content provided")
         sys.exit(1)
 elif len(sys.argv) > 1 and sys.argv[1] == MODULE_FLAG:
-    # Execute the module passed as the second argument
+    if pyi_splash and pyi_splash.is_alive():
+        pyi_splash.close()
+
     if len(sys.argv) >= MIN_ARGS_FOR_MODULE:
         module_name = sys.argv[2]
-        # Build the command to run the module with remaining arguments
         module_args = sys.argv[MIN_ARGS_FOR_MODULE:] if len(sys.argv) > MIN_ARGS_FOR_MODULE else []
-
-        # We're running as a packaged executable, run module directly
-        # Update sys.argv to what the module expects
         sys.argv = [module_name, *module_args]
         try:
             if module_name == "marimo":
-                # Special handling for marimo - importing from private module as marimo's __main__.py does
                 from marimo._cli.cli import main  # noqa: PLC2701
 
                 main(prog_name="marimo")
             else:
-                # Generic module execution
                 import runpy
 
                 runpy.run_module(module_name, run_name="__main__")
@@ -64,9 +71,13 @@ elif len(sys.argv) > 1 and sys.argv[1] == MODULE_FLAG:
         logger.error("No module name provided")
         sys.exit(1)
 elif len(sys.argv) > 1 and sys.argv[1] == DEBUG_FLAG:
+    if pyi_splash and pyi_splash.is_alive():
+        pyi_splash.close()
+
     import ssl
 
     print(ssl.get_default_verify_paths())
 else:
-    # Normal GUI launch
+    if pyi_splash and pyi_splash.is_alive():
+        pyi_splash.update_text("Opening user interface ...")
     gui_run(native=True, with_api=False, title="Aignostics Launchpad", icon="🔬")