Feat/bridge (#258)

* refactor(utils): introduce library mode inc. auto-detection
* refactor(utils): don't initialize sentry, logfire, ssl trust store or certifi in library mode
* refactor(utils): lower log level of boot message
* refactor(utils): introduce loguru
* refactor(utils): remove logfire
* chore(release): start to adapt expected output for heta update
* chore(deps): bump
* test(utils): add missing unit test marker

Author: helmut-hoffer-von-ankershoffen

.env.example

@@ -3,9 +3,7 @@ AIGNOSTICS_SYSTEM_TOKEN=YOUR_SECRET_TOKEN
 AIGNOSTICS_LOG_LEVEL=INFO
 AIGNOSTICS_LOG_FILE_ENABLED=false
 AIGNOSTICS_LOG_FILE_NAME=aignostics.log
-AIGNOSTICS_LOG_CONSOLE_ENABLED=false
-AIGNOSTICS_LOGFIRE_ENABLED=false
-AIGNOSTICS_LOGFIRE_INSTRUMENT_SYSTEM_METRICS=true
+AIGNOSTICS_LOG_STDERR_ENABLED=false
 AIGNOSTICS_SENTRY_ENABLED=false
 AIGNOSTICS_SENTRY_DEBUG=false
 AIGNOSTICS_SENTRY_SEND_DEFAULT_PII=false

.github/workflows/_install_dev_tools.bash

@@ -11,7 +11,7 @@ log() {
 log "Starting installation of development tools..."
 
 # Disable man-db updates to speed up package installation
-sudo rm /var/lib/man-db/auto-update
+sudo rm -f /var/lib/man-db/auto-update
 
 # Install APT packages
 wget -qO - https://aquasecurity.github.io/trivy-repo/deb/public.key | sudo apt-key add -

ATTRIBUTIONS.md

@@ -506,40 +506,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## aignostics (0.2.192) - MIT License
-
-🔬 Python SDK providing access to the Aignostics Platform. Includes Aignostics Launchpad (Desktop Application), Aignostics CLI (Command-Line Interface), example notebooks, and Aignostics Client Library.
-
-* URL: https://aignostics.readthedocs.io/en/latest/
-* Author(s): Helmut Hoffer von Ankershoffen <[email protected]>, Andreas Kunft <[email protected]>
-
-### License Text
-
-```
-MIT License
-
-Copyright (c) [2025] [Aignostics GmbH ([email protected])]
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-```
-
 ## aiofile (3.9.0) - Apache Software License
 
 Asynchronous file operations.
@@ -1760,6 +1726,40 @@ IN THE SOFTWARE.
 
 ```
 
+## annotated-doc (0.0.3) - MIT License
+
+Document parameters, class attributes, return types, and variables inline, with Annotated.
+
+* URL: https://github.com/fastapi/annotated-doc
+* Author(s): Sebastián Ramírez
+
+### License Text
+
+```
+The MIT License (MIT)
+
+Copyright (c) 2025 Sebastián Ramírez
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+```
+
 ## annotated-types (0.7.0) - MIT License
 
 Reusable constraint types to use with typing.Annotated
@@ -3659,7 +3659,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## boto3 (1.40.51) - Apache Software License
+## boto3 (1.40.59) - Apache-2.0
 
 The AWS SDK for Python
 
@@ -3857,7 +3857,7 @@ Copyright 2013-2017 Amazon.com, Inc. or its affiliates. All Rights Reserved.
 
 ```
 
-## botocore (1.40.51) - Apache-2.0
+## botocore (1.40.59) - Apache-2.0
 
 Low-level, data-driven core of boto 3.
 
@@ -7585,7 +7585,7 @@ SOFTWARE.
 
 ```
 
-## fastapi (0.119.0) - MIT License
+## fastapi (0.120.0) - MIT License
 
 FastAPI framework, high performance, easy to learn, fast to code, ready for production
 
@@ -10400,7 +10400,7 @@ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 
 ```
 
-## humanize (4.13.0) - UNKNOWN
+## humanize (4.14.0) - UNKNOWN
 
 Python humanize utilities
 
@@ -12606,7 +12606,7 @@ license-expression is a comprehensive utility library to parse, compare, simplif
 
 ```
 
-## logfire (4.13.2) - UNKNOWN
+## logfire (4.14.2) - UNKNOWN
 
 The best Python observability tool! 🪵🔥
 
@@ -12794,7 +12794,7 @@ Copyright 2010-2020 - Ronald Oussoren
 
 ```
 
-## marimo (0.16.5) - Apache Software License
+## marimo (0.17.2) - Apache Software License
 
 A library for making reactive notebooks and apps
 
@@ -13272,12 +13272,12 @@ Copyright (C) 2008-2011 INADA Naoki <[email protected]>
 
 ```
 
-## msgspec (0.19.0) - BSD License
+## msgspec_m (0.19.2) - BSD License
 
 A fast serialization and validation library, with builtin support for JSON, MessagePack, YAML, and TOML.
 
-* URL: https://jcristharif.com/msgspec/
-* Maintainer(s): Jim Crist-Harif
+* URL: https://github.com/marimo-team/msgspec
+* Maintainer(s): marimo team
 
 ### License Text
 
@@ -13855,7 +13855,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## nicegui (3.0.4) - MIT License
+## nicegui (3.1.0) - MIT License
 
 Create web-based user interfaces with Python. The nice way.
 
@@ -14020,7 +14020,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## nox (2025.5.1) - UNKNOWN
+## nox (2025.10.16) - UNKNOWN
 
 Flexible test automation.
 
@@ -24654,7 +24654,7 @@ Proxy Implementation
 * URL: http://github.com/jtushman/proxy_tools
 * Author(s): Jonathan Tushman
 
-## psutil (7.1.0) - BSD-3-Clause
+## psutil (7.1.2) - BSD-3-Clause
 
 Cross-platform lib for process and system monitoring.
 
@@ -28387,7 +28387,7 @@ C version of reader, parser and emitter for ruamel.yaml derived from libyaml
 
 ```
 
-## ruff (0.14.0) - MIT License
+## ruff (0.14.2) - MIT License
 
 An extremely fast Python linter and code formatter, written in Rust.
 
@@ -29563,7 +29563,7 @@ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 ```
 
-## sentry-sdk (2.41.0) - BSD License
+## sentry-sdk (2.42.1) - BSD License
 
 Python client for Sentry (https://sentry.io)
 
@@ -31791,7 +31791,7 @@ SOFTWARE.
 
 ```
 
-## typer (0.19.2) - MIT License
+## typer (0.20.0) - MIT License
 
 Typer, build great CLIs. Easy to code. Based on Python type hints.
 
@@ -33192,7 +33192,7 @@ SOFTWARE.
 
 ```
 
-## uv (0.9.2) - Apache Software License; MIT License
+## uv (0.9.5) - Apache Software License; MIT License
 
 An extremely fast Python package and project manager, written in Rust.
 

CLI_REFERENCE.md

@@ -14,7 +14,7 @@ $ aignostics [OPTIONS] COMMAND [ARGS]...
 * `--show-completion`: Show completion for the current shell, to copy it or customize the installation.
 * `--help`: Show this message and exit.
 
-🔬 Aignostics Python SDK v0.2.195 - built with love in Berlin 🐻
+🔬 Aignostics Python SDK v0.2.199 - built with love in Berlin 🐻
 
 **Commands**:
 
@@ -204,7 +204,7 @@ $ aignostics application run execute [OPTIONS] APPLICATION_ID METADATA_CSV_FILE
 * `--application-version TEXT`: Version of the application. If not provided, the latest version will be used.
 * `--create-subdirectory-for-run / --no-create-subdirectory-for-run`: Create a subdirectory for the results of the run in the destination directory  [default: create-subdirectory-for-run]
 * `--create-subdirectory-per-item / --no-create-subdirectory-per-item`: Create a subdirectory per item in the destination directory  [default: create-subdirectory-per-item]
-* `--upload-prefix TEXT`: Prefix for the upload destination. If not given will be set to current milliseconds.  [default: 1761499056785.385]
+* `--upload-prefix TEXT`: Prefix for the upload destination. If not given will be set to current milliseconds.  [default: 1763046365825.4631]
 * `--wait-for-completion / --no-wait-for-completion`: Wait for run completion and download results incrementally  [default: wait-for-completion]
 * `--note TEXT`: Optional note to include with the run submission via custom metadata.
 * `--due-date TEXT`: Optional soft due date to include with the run submission, ISO8601 format. The scheduler will try to complete the run by this date, taking the subscription tierand available GPU resources into account.
@@ -267,7 +267,7 @@ $ aignostics application run upload [OPTIONS] APPLICATION_ID METADATA_CSV_FILE
 **Options**:
 
 * `--application-version TEXT`: Version of the application. If not provided, the latest version will be used.
-* `--upload-prefix TEXT`: Prefix for the upload destination. If not given will be set to current milliseconds.  [default: 1761499056785.492]
+* `--upload-prefix TEXT`: Prefix for the upload destination. If not given will be set to current milliseconds.  [default: 1763046365825.575]
 * `--onboard-to-aignostics-portal / --no-onboard-to-aignostics-portal`: If set, the run will be onboarded to the Aignostics Portal.  [default: no-onboard-to-aignostics-portal]
 * `--help`: Show this message and exit.
 

noxfile.py

@@ -408,8 +408,8 @@ def _generate_openapi_schemas(session: nox.Session) -> None:
     Path("docs/source/_static").mkdir(parents=True, exist_ok=True)
 
     formats = {
-        "yaml": {"ext": "yaml", "args": ["--output-format=yaml", "--env", "AIGNOSTICS_LOG_CONSOLE_ENABLED=false"]},
-        "json": {"ext": "json", "args": ["--output-format=json", "--env", "AIGNOSTICS_LOG_CONSOLE_ENABLED=false"]},
+        "yaml": {"ext": "yaml", "args": ["--output-format=yaml", "--env", "AIGNOSTICS_LOG_STDERR_ENABLED=false"]},
+        "json": {"ext": "json", "args": ["--output-format=json", "--env", "AIGNOSTICS_LOG_STDERR_ENABLED=false"]},
     }
 
     for version in API_VERSIONS:
@@ -443,7 +443,7 @@ def _generate_sdk_metadata_schema(session: nox.Session, schema_type: str) -> Non
             f"{schema_type}-metadata-schema",
             "--no-pretty",
             "--env",
-            "AIGNOSTICS_LOG_CONSOLE_ENABLED=false",
+            "AIGNOSTICS_LOG_STDERR_ENABLED=false",
             stdout=f,
             external=True,
         )
@@ -935,7 +935,7 @@ def setup(session: nox.Session) -> None:
         session.run("git", "add", ".", external=True)
         try:
             session.run("pre-commit", external=True)
-        except Exception:  # noqa: BLE001
+        except Exception:
             session.log("pre-commit run failed, continuing anyway")
         session.run("git", "add", ".", external=True)
 

pyproject.toml

@@ -74,45 +74,37 @@ requires-python = ">=3.11, <3.14"
 
 dependencies = [
     # From Template
-    "fastapi[standard,all]>=0.120.4,<1",
+    "fastapi[standard,all]>=0.121.1,<1",
     "humanize>=4.14.0,<5",
-    "logfire[system-metrics]>=4.14.2,<5",
     "nicegui[native]>=3.1.0,<3.2.0", # Regression in 3.2.0
-    "opentelemetry-instrumentation-fastapi>=0.53b0,<1",
-    "opentelemetry-instrumentation-httpx>=0.53b0,<1",
-    "opentelemetry-instrumentation-jinja2>=0.53b0,<1",
-    "opentelemetry-instrumentation-requests>=0.53b0,<1",
-    "opentelemetry-instrumentation-sqlite3>=0.53b0,<1",
-    "opentelemetry-instrumentation-tornado>=0.53b0,<1",
-    "opentelemetry-instrumentation-urllib>=0.53b0,<1",
-    "opentelemetry-instrumentation-urllib3>=0.53b0,<1",
     "packaging>=25.0,<26",
     "platformdirs>=4.5.0,<5",
-    "psutil>=7.1.2,<8",
-    "pydantic-settings>=2.11.0,<3",
+    "psutil>=7.1.3,<8",
+    "pydantic-settings>=2.12.0,<3",
     "pywin32>=310,<311 ; sys_platform == 'win32'",
     "pyyaml>=6.0.3,<7",
-    "sentry-sdk>=2.43.0,<3",
+    "sentry-sdk>=2.44.0,<3",
     "typer>=0.20.0,<1",
     "uptime>=3.0.1,<4",
     # Custom
     "aiopath>=0.6.11,<1",
-    "boto3>=1.40.64,<2",
-    "certifi>=2025.10.5,<2026",
+    "boto3>=1.40.61,<2",
+    "certifi>=2025.11.12,<2026",
     "defusedxml>=0.7.1",
     "dicom-validator>=0.7.3,<1",
     "dicomweb-client[gcp]>=0.59.3,<1",
     "duckdb>=0.10.0,<=1.4.1",
     "fastparquet>=2024.11.0,<2025",
-    "google-cloud-storage>=3.4.1,<4",
+    "google-cloud-storage>=3.5.0,<4",
     "google-crc32c>=1.7.1,<2",
     "highdicom>=0.26.1,<1",
     "html-sanitizer>=2.6.0,<3",
     "httpx>=0.28.1,<1",
-    "idc-index-data==22.0.2",
+    "idc-index-data==22.1.2",
     "ijson>=3.4.0.post0,<4",
     "jsf>=0.11.2,<1",
     "jsonschema[format-nongpl]>=4.25.1,<5",
+    "loguru>=0.7.3",
     "openslide-bin>=4.0.0.8,<5",
     "openslide-python>=1.4.2,<2",
     "pandas>=2.3.3,<3",
@@ -138,8 +130,8 @@ pyinstaller = ["pyinstaller>=6.14.0,<7"]
 jupyter = ["jupyter>=1.1.1,<2"]
 marimo = [
     "cloudpathlib>=0.23.0,<1",
-    "ipython>=9.6.0,<10",
-    "marimo>=0.17.2,<1",
+    "ipython>=9.7.0,<10",
+    "marimo>=0.17.7,<1",
     "matplotlib>=3.10.7,<4",
     "shapely>=2.1.0,<3",
 ]
@@ -154,15 +146,15 @@ dev = [
     "furo>=2025.9.25,<2026",
     "git-cliff>=2.10.1,<3",
     "mypy>=1.18.2,<2",
-    "nox[uv]>=2025.10.16,<2026",
+    "nox[uv]>=2025.11.12,<2026",
     "pip-audit>=2.9.0,<3",
     "pip-licenses @ git+https://github.com/neXenio/pip-licenses.git@master", # https://github.com/raimon49/pip-licenses/pull/224
-    "pre-commit>=4.3.0,<5",
+    "pre-commit>=4.4.0,<5",
     "pyright>=1.1.406,<1.1.407", # Regression in 1.1.407, see https://github.com/microsoft/pyright/issues/11060
     "pytest>=8.4.2,<9",
-    "pytest-asyncio>=1.2.0,<2",
+    "pytest-asyncio>=1.3.0,<2",
     "pytest-cov>=7.0.0,<8",
-    "pytest-docker>=3.2.3,<4",
+    "pytest-docker>=3.2.5,<4",
     "pytest-durations>=1.6.1,<2",
     "pytest-env>=1.2.0,<2",
     "pytest-md-report>=0.7.0,<1",
@@ -173,7 +165,7 @@ dev = [
     "pytest-timeout>=2.4.0,<3",
     "pytest-watcher>=0.4.3,<1",
     "pytest-xdist[psutil]>=3.8.0,<4",
-    "ruff>=0.14.3,<1",
+    "ruff>=0.14.4,<1",
     "scalene>=1.5.55,<2",
     "sphinx>=8.2.3,<9",
     "sphinx-autobuild>=2025.8.25,<2026",
@@ -275,6 +267,7 @@ ignore = [
     "PTH123",   # use of open to be replaced with Path.open,
     "T201",     # Remove `print`
     "INP001",   # Checks for packages that are missing an __init__.py file.
+    "BLE001",   # Accept for now TODO(Helmut): Add proper exception handling later
 ]
 
 [tool.ruff.lint.per-file-ignores]