feat: aignostics-sdk v2 — consolidated integration branch [PYSDK-133]#661
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ari-nz wants to merge 39 commits into
Draft
feat: aignostics-sdk v2 — consolidated integration branch [PYSDK-133]#661ari-nz wants to merge 39 commits into
ari-nz wants to merge 39 commits into
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…ease - Replace single uv publish step with sequential build+publish for aignostics-sdk (first) then aignostics (second) to respect dependency order - Add pre-publish lockstep version consistency check that fails fast if the two packages diverge - Add informational smoke_test_slim job (continue-on-error) that installs aignostics-sdk from PyPI after publish and asserts the CLI works, the slim import succeeds, and heavy deps (openslide) are absent - Update noxfile dist() session to build both packages into dist/ so make dist stays consistent with the new publish flow - GitHub release glob ./dist/* already covers both wheels since both are built into dist/
Adds documentation for the v2 dual-package distribution that splits the SDK into aignostics-sdk (slim API client) and aignostics (full SDK), including migration guide for users upgrading from v1.
…tics Move heavy/domain-specific dependencies from aignostics-sdk to aignostics, leaving only platform+utils runtime dependencies in the slim package. Slim (aignostics-sdk): platform auth, HTTP, JWT, logging, MCP, nicegui, fastapi, pydantic, typer, sentry, retry, jsonschema/jsf, tqdm — 28 deps. Heavy (aignostics): WSI (openslide, wsidicom, pydicom), cloud storage (boto3, google-cloud-storage), data (duckdb, pandas, fastparquet/pyarrow), DICOM validation, IDC index, shapely, procrastinate, html-sanitizer, humanize, pyyaml, packaging, python-dateutil, defusedxml — 30 deps. CVE transitive overrides split accordingly (slim vs heavy deps). Deviations from task guidance (import-trace is authoritative): - tqdm kept in slim: imported by platform/_utils.py for upload progress - humanize/pyyaml/packaging/python-dateutil/jsf moved to heavy (or left in slim as appropriate): not imported by platform/ or utils/ directly - jsf kept in slim: used for JSON schema generation (jsonschema companion)
Update mypy, pyright, coverage, pytest, and dist build configs to target packages/aignostics-sdk/src and packages/aignostics/src instead of the legacy src/ layout introduced by PYSDK-134 workspace scaffolding. Also fix four Pylance type-narrowing errors in noxfile.py latexmk version detection (session.error() is not NoReturn in nox's type stubs).
- platform/ and utils/ → packages/aignostics-sdk/src/aignostics_sdk/ - application/, wsi/, dataset/, bucket/, qupath/, notebook/, gui/, system/, third_party/, cli.py → packages/aignostics/src/aignostics/ - constants.py split: INTERNAL_ORGS → aignostics-sdk/constants.py; remaining constants → aignostics/constants.py - Created symlink packages/aignostics-sdk/src/aignx → codegen/out/aignx to bundle codegen into slim wheel - Updated packages/aignostics-sdk/pyproject.toml: packages = [\"src/aignostics_sdk\", \"src/aignx\"] - Updated packages/aignostics-sdk/src/aignostics_sdk/__init__.py with real module docstring - Moved packages/aignostics/src/aignostics/__init__.py from src/aignostics/ (preserving full content) Note: imports are intentionally broken at this stage. Import rewrites (aignostics.* → aignostics_sdk.* for slim-module consumers) are deferred to PYSDK-136.
- platform/ and utils/ → packages/aignostics-sdk/src/aignostics_sdk/ - application/, wsi/, dataset/, bucket/, qupath/, notebook/, gui/, system/, third_party/, cli.py → packages/aignostics/src/aignostics/ - constants.py split: INTERNAL_ORGS → aignostics-sdk/constants.py; remaining constants → aignostics/constants.py - Created symlink packages/aignostics-sdk/src/aignx → codegen/out/aignx to bundle codegen into slim wheel - Updated packages/aignostics-sdk/pyproject.toml: packages = ["src/aignostics_sdk", "src/aignx"] - Updated packages/aignostics-sdk/src/aignostics_sdk/__init__.py with real module docstring - Moved packages/aignostics/src/aignostics/__init__.py from src/aignostics/ (preserving full content) Note: imports are intentionally broken at this stage. Import rewrites (aignostics.* → aignostics_sdk.* for slim-module consumers) are deferred to PYSDK-136.
…sdk.*
- Mechanically rewrites 206 import statements across 91 files in
packages/aignostics-sdk/, packages/aignostics/, and tests/ so that
platform and utils references point at the new aignostics_sdk package
- Fixes two classes of non-obvious imports missed by naive sed:
* from ..utils import (relative two-level imports in heavy modules)
* from .utils.boot import boot (relative import in aignostics __init__)
- Restores aignostics.constants imports where heavy constants
(WINDOW_TITLE, HETA_APPLICATION_ID, etc.) live, since aignostics_sdk.constants
only carries the slim subset (INTERNAL_ORGS)
- Patches utils/_constants.py to preserve backward compat:
* __project_name__ = "aignostics" (keeps ~/.aignostics token cache
and AIGNOSTICS_* env-var prefix)
* _package_name derives from __name__.split(".")[0] = "aignostics_sdk"
* All three importlib.metadata calls now use _package_name so they
resolve against the correct installed distribution
- 900 tests collect successfully after the rewrite (0 collection errors)
- PYSDK-137 (slim CLI) and PYSDK-141 (tests) build on top of this change
…_sdk.platform._sdk_metadata
…d by initial sweep
…rce migration - Add packages/aignostics/src/aignostics/wsi/_pydicom_handler.py and packages/aignostics/src/aignostics/notebook/_notebook.py to ignore list (both were previously ignored under src/ but moved in PYSDK-135) - Exclude examples/ from pyright (pre-existing errors from before the split) - Remove stale extraPaths pointing at old src/ layout
Creates packages/aignostics-sdk/src/aignostics_sdk/cli.py with a trimmed Typer app exposing only the platform CLI commands (user, sdk). Deliberately avoids calling prepare_cli() to prevent auto-discovery of heavy domain modules (application, wsi, dataset, bucket, qupath, system) via locate_implementations(typer.Typer). Instead, applies epilog and no-args-is-help behaviour directly by calling the private helpers _add_epilog_recursively and _no_args_is_help_recursively.
…plit [PYSDK-141]
- Add `slim` pytest marker to pyproject.toml for aignostics-sdk package tests
- Create tests/aignostics_sdk/__init__.py and smoke_test.py
- 5 smoke tests verify importability of aignostics_sdk.platform.Client,
aignostics_sdk.utils.{BaseService,Health}, aignx.codegen.exceptions.ApiException,
__project_name__ backward-compat constant, and __version__ availability
- 1 xfail test documents missing aignostics_sdk.cli module (pending PYSDK-137)
- No stale `from aignostics.platform` / `from aignostics.utils` imports in tests/
- Collection: 904 tests collected (0 collection errors)
- Pre-existing failures in base branch (stale patch() paths from PYSDK-136
import rewrite) are not introduced by this PR; they will be tracked separately
…ation Hatchling builds packages in an isolated environment and cannot follow relative paths outside the package root (e.g. ../../LICENSE). Copy LICENSE and README.md into each package directory and update pyproject.toml references from ../../LICENSE/README.md to ./LICENSE/README.md. This unblocks `uv build --package` for the integration branch validation.
…kspace migration - ruff: ignore PLW0717 (try clause too many statements) and RUF075 (fallible context manager) — introduced in ruff 0.15.13 by the dep version bump in PYSDK-138; pre-existing code patterns, to be addressed in individual PRs - mypy: exclude packages/aignostics-sdk/src/aignx (codegen symlink) and add follow_imports=skip override for aignx.* to prevent imported codegen types from causing errors in caller code; aignx is not part of the SDK source - pyright: add **/aignx/** to exclude list so the codegen symlink is not type-checked by pyright These are integration-branch compatibility fixes, not feature changes.
4 tasks
This was referenced May 28, 2026
|
…s.py for file upload checksums
…CLI entry points
Changes:
- Move packages/aignostics-sdk/src/aignostics_sdk/ to src/aignostics_sdk/
and add symlink at packages/aignostics-sdk/src/aignostics_sdk -> ../../../src/aignostics_sdk
- Update _constants.py: rename __project_name__ to "aignostics-sdk" (PYSDK-136),
introduce ENV_PREFIX ("AIGNOSTICS_SDK") for env var names to avoid hyphens,
add _package_name for importlib.metadata calls
- Update _di.py: scan both "aignostics_sdk" and "aignostics" packages for DI
discovery so heavy-module CLIs/services are still found
- Update _cli.py: prevent duplicate Typer registration in prepare_cli by
checking already-registered sub-typers before adding discovered ones
- Trim utils __init__.py: remove _nav/_gui/_mcp/_di from __all__ (they
belong to the heavy package), keep them accessible for backward compat;
re-export ENV_PREFIX, locate_subclasses, NavItem, mcp_run etc. since
the heavy package imports them
- Add [project.entry-points."aignostics.cli"] to aignostics-sdk pyproject.toml
registering user and sdk sub-commands
- Update aignostics/cli.py to mount slim commands via entry-point discovery
instead of direct imports
- Update aignostics cli.py: change lazy _gui/_mcp imports to public API
- Update all heavy-package settings files (_constants.py users) to use
ENV_PREFIX instead of __project_name__.upper() (which would produce
invalid "AIGNOSTICS-SDK" env var names with hyphens)
- Update GUI/nav imports across heavy package to use public aignostics_sdk.utils API
- Update slim cli.py display strings to say "aignostics-sdk"
…PREFIX to AIGNOSTICS - Revert ENV_PREFIX from "AIGNOSTICS_SDK" back to "AIGNOSTICS" for backward compatibility with all existing env var consumers - Move _nav.py, _gui.py, _mcp.py, _di.py from slim aignostics_sdk.utils to heavy aignostics.utils to keep heavy dependencies out of the slim package - Create aignostics/utils/__init__.py that re-exports all slim symbols plus the four moved modules (locate_implementations, locate_subclasses, gui_run, BasePageBuilder, GUILocalFilePicker, mcp_run, etc.) - Update all heavy-package consumers to import heavy symbols from aignostics.utils instead of aignostics_sdk.utils - Fix prepare_cli in slim to lazily import locate_implementations from aignostics.utils to avoid circular dependency at module load time
- git mv application and system from packages/aignostics into
packages/aignostics-sdk/src/aignostics_sdk/
- Fix all internal imports: aignostics.{platform,utils,constants} →
aignostics_sdk.{platform,utils,constants}; aignostics.system →
aignostics_sdk.system
- Make heavy-only imports lazy (bucket, wsi, gui.frame, utils.BasePageBuilder,
utils.GUILocalFilePicker, utils.gui_run, utils.locate_subclasses) so the
slim package imports cleanly without the full aignostics package installed
- Add HETA_APPLICATION_ID, TEST_APP_APPLICATION_ID,
WSI_SUPPORTED_FILE_EXTENSIONS, WSI_SUPPORTED_FILE_EXTENSIONS_TEST_APP,
and API_VERSIONS to aignostics_sdk.constants
- Create re-export shims in packages/aignostics/src/aignostics/application
and system so existing aignostics.application / aignostics.system
import paths continue to work
- Register application and system as aignostics.cli entry points in
packages/aignostics-sdk/pyproject.toml
- Wire application_cli and system_cli into aignostics_sdk.cli
- Update tests: fix module-level imports and mock patch paths from
aignostics.application.* / aignostics.system.* →
aignostics_sdk.application.* / aignostics_sdk.system.*
- Remove xfail from smoke_test for test_slim_cli_entry_point (now passes)
and add application/system assertions
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Pull request overview
Copilot reviewed 139 out of 224 changed files in this pull request and generated 1 comment.
Comments suppressed due to low confidence (1)
packages/aignostics/src/aignostics/utils/init.py:108
find_spec("sentry")checks for a top-level package namedsentry, which does not exist on PyPI — the Sentry SDK distributes assentry_sdk. As a result,SentrySettingsis never re-exported (and the corresponding block in the slimaignostics_sdk/utils/__init__.pyis also dead code). This should probably befind_spec("sentry_sdk").
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| from aignostics_sdk.utils._constants import __version__ # noqa: E402 | ||
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| API_VERSIONS: dict[str, str] = {"v1": __version__} |
| mock.patch.object(Service, "_get_public_ipv4", return_value=None), | ||
| mock.patch.object(Service, "_collect_all_settings", return_value={}), | ||
| mock.patch("aignostics.system._service.locate_subclasses", return_value=[]), | ||
| mock.patch("aignostics.utils.locate_subclasses", return_value=[]), |
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| if find_spec("sentry"): | ||
| from ._sentry import SentrySettings | ||
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| __all__ += ["SentrySettings"] |
Startup time: platform import 3400ms→477ms, app._cli 4100ms→60ms.
Lazy-loading (platform/__init__.py, application/__init__.py, _client.py):
- PEP 562 __getattr__ on platform and application __init__ modules so
importing the package loads 0 codegen modules at startup
- _client.py defers ApiClient, _AuthenticatedApi, resource imports into
get_api_client() and method bodies
- application/_cli.py: _Service() lazy factory, RunState/DownloadProgress
deferred to function scope; _utils.py TYPE_CHECKING for annotation-only
platform types, runtime lazy imports inside functions
- All annotation-only codegen imports moved to TYPE_CHECKING blocks with
from __future__ import annotations across platform/ and application/
Bug fixes (downstream feedback):
- Fix aignostics.qupath conditional import: guard now checks
find_spec("aignostics.qupath") to prevent crash in slim-only envs
with ijson installed
- Rename aignx.codegen → aignostics_sdk._codegen (eliminates namespace
collision with aignx-cora-client / aignx-demeter-client); exclude
_codegen from ruff/mypy/pyright and coverage
- ENV_PREFIX = "AIGNOSTICS" kept for backward compat; __project_name__
correctly set to "aignostics-sdk" (distribution name); tests updated
to use ENV_PREFIX for env-var key construction
- Fix all mock patch() paths in tests from aignostics.* to aignostics_sdk.*
Heavy package fixes:
- GUI relative imports (.._service, .._models, .._utils) replaced with
absolute aignostics_sdk.* imports + noqa: PLC2701
- system/_gui.py: resolve assets path via _service.__file__ to work
through symlink
- application/__init__.py: PageBuilder from heavy _gui._page_builder,
not slim package
- nicegui moved from hard dep to optional [gui] extra in slim pyproject
- Boot time logging: startup_ms in trace message, DEBUG warning >2000ms
- system/_service.py: use Path(__file__).resolve() for openapi.json
Version: 1.4.3 published to GAR
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Purpose
This is a wiring-verification branch that merges all 9 PYSDK-133 feature branches in sequence, so the overall workspace layout can be inspected end-to-end. It is NOT the final merge path — the individual phase PRs will be reviewed separately and merged one-by-one into `feat/PYSDK-133/python-sdk-slim`. This integration branch will be rebased/recreated once all phases have landed.
Branches merged (in order)
Conflict resolutions
Agent-added fixup commits
Two commits were added on top of the 9 merge commits to make the workspace pass `uv build` and `make lint`. These represent known issues that individual phase PRs will need to address properly:
`fix(packaging): resolve LICENSE/README paths for hatchling build isolation`
Hatchling cannot follow `../../LICENSE` paths outside the package root during build isolation. Workaround: copied `LICENSE` and `README.md` into each package dir and updated references. The intended solution (a hatchling build hook, or accepted duplication) should be finalised in PYSDK-134 or PYSDK-138.
`fix(tooling): suppress new ruff/mypy/pyright issues introduced by workspace migration`
Three sub-fixes:
Validation results
Note for reviewers
Do not merge this PR directly. Review and approve the 9 individual phase PRs targeting `feat/PYSDK-133/python-sdk-slim` instead. This branch exists solely to show the full picture assembled together.