feat(packaging): introduce uv workspace structure for aignostics-sdk split [PYSDK-134]

packages/aignostics-sdk/pyproject.toml

@@ -0,0 +1,181 @@
+[project]
+name = "aignostics-sdk"
+version = "1.4.0"
+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 = [
+    { name = "Helmut Hoffer von Ankershoffen", email = "[email protected]" },
+    { name = "Andreas Kunft", email = "[email protected]" },
+]
+license = { file = "../../LICENSE" }
+
+keywords = [
+    "aignostics",
+    "atlas",
+    "whole-slide-imaging",
+    "machine-learning",
+    "digital-pathology",
+    "medical-imaging",
+    "qupath",
+    "dicom",
+    "pydicom",
+    "openslide",
+    "image-data-commons",
+    "act",
+    "codecov",
+    "copier",
+    "cyclonedx",
+    "devcontainer",
+    "detect-secrets",
+    "docker",
+    "git-cliff",
+    "jupyter",
+    "marimo",
+    "mypy",
+    "nox",
+    "nicegui",
+    "oe-python-template",
+    "pip-audit",
+    "pip-licenses",
+    "pre-commit",
+    "pydantic",
+    "pytest",
+    "python",
+    "pypi",
+    "readthedocs",
+    "ruff",
+    "sonarqube",
+    "sonarcloud",
+    "sphinx",
+    "typer",
+    "uv",
+]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: End Users/Desktop",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows",
+    "Framework :: Pydantic",
+    "Framework :: Pytest",
+    "Typing :: Typed",
+    "Natural Language :: English",
+]
+
+# WARNING: The upper bound of requires-python is *not* respected by uvx
+requires-python = ">=3.11, <3.15"
+
+dependencies = [
+    # From Template
+    "fastapi[all,standard]>=0.123.10",
+    "humanize>=4.14.0,<5",
+    "nicegui[native]>=3.11.0,<4",
+    "packaging>=26,<27",
+    "platformdirs>=4.5.1,<5",
+    "psutil>=7.1.3,<8",
+    "pydantic-settings>=2.12.0,<3",
+    "pywin32>=311,<312; sys_platform == 'win32'",
+    "pyyaml>=6.0.3,<7",
+    "sentry-sdk>=2.47.0,<3",
+    "typer>=0.20.0,<1",
+    # Custom
+    "boto3>=1.42.4,<2",
+    "certifi>=2025.11.12",
+    "defusedxml>=0.7.1",
+    "dicom-validator>=0.7.3,<1",
+    "dicomweb-client[gcp]>=0.59.3,<1",
+    "duckdb>=1.4.2,<=2",
+    "google-cloud-storage>=3.6.0,<4",
+    "crc32c>=2.8,<3",
+    "highdicom>=0.26.1,<1; python_version < '3.14'",
+    "html-sanitizer>=2.6.0,<3",
+    "httpx>=0.28.1,<1",
+    "idc-index-data==24.0.3",
+    "ijson>=3.4.0.post0,<4",
+    "jsf>=0.11.2,<1",
+    "jsonschema[format-nongpl]>=4.25.1,<5",
+    "loguru>=0.7.3,<1",
+    "openslide-bin>=4.0.0.10,<5",
+    "openslide-python>=1.4.3,<2",
+    "pandas>=2.3.3,<4",
+    "platformdirs>=4.3.2,<5",
+    "procrastinate>=3.5.3",
+    "fastparquet>=2026.3.0,<2026.4.0; python_version < '3.14'",
+    "pyarrow>=23.0.1,<24; python_version >= '3.14'",
+    "pyjwt[crypto]>=2.12.0,<3",
+    "python-dateutil>=2.9.0.post0,<3",
+    "requests>=2.33.0,<3",
+    "requests-oauthlib>=2.0.0,<3",
+    "s5cmd>=0.3.3,<1",
+    "semver>=3.0.4,<4",
+    "shapely>=2.1.2,<3",
+    "tenacity>=9.1.2,<10",
+    "tqdm>=4.67.1,<5",
+    "truststore>=0.10.4,<1",
+    "urllib3>=2.6.3,<3",
+    "wsidicom>=0.28.1,<1",
+    "fastmcp>=3.2.0,<4",
+    # Transitive overrides
+    "rfc3987; sys_platform == 'never'",
+    "h11>=0.16.0",
+    "tornado>=6.5.5",
+    "urllib3>=2.5.0",
+    "pillow>=12.2.0",
+    "aiohttp>=3.13.4",
+    "starlette>=1.0.1",
+    "lxml>=6.1.0",
+    "filelock>=3.20.3",
+    "marshmallow>=3.26.2",
+    "pygments>=2.20.0",
+    "cryptography>=46.0.7",
+    "pydicom>=3.0.2",
+    "pyasn1>=0.6.3",
+    "lxml-html-clean>=0.4.4",
+    "python-multipart>=0.0.26",
+    "protobuf>=6.33.5",
+]
+
+[project.optional-dependencies]
+pyinstaller = ["pyinstaller>=6.14.0,<7"]
+jupyter = [
+    "jupyter>=1.1.1,<2",
+    "jupyter-core>=5.8.1",
+    "jupyterlab>=4.4.9",
+    "nbconvert>=7.17.1",
+]
+marimo = [
+    "cloudpathlib>=0.23.0,<1",
+    "ipython>=9.8.0,<10",
+    "marimo>=0.23.0,<1",
+    "matplotlib>=3.10.7,<4",
+    "shapely>=2.1.0,<3",
+]
+qupath = []
+
+[project.scripts]
+aignostics-sdk = "aignostics_sdk.cli:cli"
+
+[build-system]
+requires = ["hatchling==1.29.0"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build]
+include = ["src/*"]
+# TODO(Phase 5): Bundle codegen/out/aignx into wheel. Hatchling does not support
+# paths outside the project root (../../codegen/out/*). Options: symlink, copy
+# via a build hook, or use a hatch plugin. Deferred to the codegen migration phase.
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/aignostics_sdk"]
+
+[tool.hatch.metadata]
+allow-direct-references = true

packages/aignostics-sdk/src/aignostics_sdk/__init__.py

@@ -0,0 +1 @@
+"""Package stub — source migrated in Phase 2."""

packages/aignostics/pyproject.toml

@@ -0,0 +1,123 @@
+[project]
+name = "aignostics"
+version = "1.4.0"
+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 = [
+    { name = "Helmut Hoffer von Ankershoffen", email = "[email protected]" },
+    { name = "Andreas Kunft", email = "[email protected]" },
+]
+license = { file = "../../LICENSE" }
+
+keywords = [
+    "aignostics",
+    "atlas",
+    "whole-slide-imaging",
+    "machine-learning",
+    "digital-pathology",
+    "medical-imaging",
+    "qupath",
+    "dicom",
+    "pydicom",
+    "openslide",
+    "image-data-commons",
+    "act",
+    "codecov",
+    "copier",
+    "cyclonedx",
+    "devcontainer",
+    "detect-secrets",
+    "docker",
+    "git-cliff",
+    "jupyter",
+    "marimo",
+    "mypy",
+    "nox",
+    "nicegui",
+    "oe-python-template",
+    "pip-audit",
+    "pip-licenses",
+    "pre-commit",
+    "pydantic",
+    "pytest",
+    "python",
+    "pypi",
+    "readthedocs",
+    "ruff",
+    "sonarqube",
+    "sonarcloud",
+    "sphinx",
+    "typer",
+    "uv",
+]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Intended Audience :: End Users/Desktop",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows",
+    "Framework :: Pydantic",
+    "Framework :: Pytest",
+    "Typing :: Typed",
+    "Natural Language :: English",
+]
+
+# WARNING: The upper bound of requires-python is *not* respected by uvx
+requires-python = ">=3.11, <3.15"
+
+dependencies = [
+    "aignostics-sdk==1.4.0",
+    # Heavy deps will be moved here from aignostics-sdk in Phase 5
+]
+
+[project.optional-dependencies]
+pyinstaller = ["pyinstaller>=6.14.0,<7"]
+jupyter = [
+    "jupyter>=1.1.1,<2",
+    "jupyter-core>=5.8.1",
+    "jupyterlab>=4.4.9",
+    "nbconvert>=7.17.1",
+]
+marimo = [
+    "cloudpathlib>=0.23.0,<1",
+    "ipython>=9.8.0,<10",
+    "marimo>=0.23.0,<1",
+    "matplotlib>=3.10.7,<4",
+    "shapely>=2.1.0,<3",
+]
+qupath = []
+
+[project.scripts]
+aignostics = "aignostics.cli:cli"
+
+[project.urls]
+Homepage = "https://aignostics.readthedocs.io/en/latest/"
+Documentation = "https://aignostics.readthedocs.io/en/latest/"
+Source = "https://github.com/aignostics/python-sdk"
+Changelog = "https://github.com/aignostics/python-sdk/releases"
+Issues = "https://github.com/aignostics/python-sdk/issues"
+
+[build-system]
+requires = ["hatchling==1.29.0"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build]
+include = ["src/*"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/aignostics"]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.uv.sources]
+aignostics-sdk = { workspace = true }

packages/aignostics/src/aignostics/__init__.py

@@ -0,0 +1 @@
+"""Package stub — source migrated in Phase 2."""