feat(packaging): migrate source into workspace package directories [PYSDK-135] by ari-nz · Pull Request #656 · aignostics/python-sdk

ari-nz · 2026-05-28T11:04:49Z

Release Train — PYSDK-133

Verify wiring on the integration branch first: #661 (draft, targets main)

Step	PR	Jira	Phase	Notes
1	#653	PYSDK-134	Workspace scaffolding	Merge first — gates everything below
2a	#656	PYSDK-135	Source migration	After #653
2b	#655	PYSDK-138	Dependency split	After #653, parallel with 2a
2c	#654	PYSDK-139	Tooling updates	After #653, parallel with 2a
3	#657	PYSDK-136	Import rewrite	After #656
4a	#658	PYSDK-137	Slim CLI	After #657
4b	#659	PYSDK-141	Tests	After #657, parallel with 4a
∞	#651	PYSDK-140	CI/CD pipeline	Independent — merge any time
∞	#652	PYSDK-142	Docs & migration	Independent — merge any time

Retargeting: each PR currently targets its predecessor branch. After the predecessor merges into feat/PYSDK-133/python-sdk-slim, retarget this PR to feat/PYSDK-133/python-sdk-slim before merging it.

This PR — Step 2a: Merge after #653 (workspace scaffolding). Retarget to feat/PYSDK-133/python-sdk-slim first. #657 (import rewrite) depends on this.

Summary

Physically moves all source files from src/aignostics/ into their new workspace package homes. Implements PYSDK-135 (Phase 2 of the aignostics-sdk slim-package split).

Note: imports are intentionally broken after this PR. Import rewrites (aignostics.* → aignostics_sdk.* for slim-module consumers) are deferred to PYSDK-136.

What moved where

→ `packages/aignostics-sdk/src/aignostics_sdk/` (slim package)

src/aignostics/platform/ → packages/aignostics-sdk/src/aignostics_sdk/platform/
src/aignostics/utils/ → packages/aignostics-sdk/src/aignostics_sdk/utils/
INTERNAL_ORGS constant extracted from src/aignostics/constants.py → packages/aignostics-sdk/src/aignostics_sdk/constants.py
packages/aignostics-sdk/src/aignostics_sdk/__init__.py stub replaced with real module docstring

→ `packages/aignostics/src/aignostics/` (full package)

src/aignostics/application/ → packages/aignostics/src/aignostics/application/
src/aignostics/wsi/ → packages/aignostics/src/aignostics/wsi/
src/aignostics/dataset/ → packages/aignostics/src/aignostics/dataset/
src/aignostics/bucket/ → packages/aignostics/src/aignostics/bucket/
src/aignostics/qupath/ → packages/aignostics/src/aignostics/qupath/
src/aignostics/notebook/ → packages/aignostics/src/aignostics/notebook/
src/aignostics/gui/ → packages/aignostics/src/aignostics/gui/
src/aignostics/system/ → packages/aignostics/src/aignostics/system/
src/aignostics/third_party/ → packages/aignostics/src/aignostics/third_party/
src/aignostics/cli.py → packages/aignostics/src/aignostics/cli.py
src/aignostics/constants.py (full) → packages/aignostics/src/aignostics/constants.py
src/aignostics/__init__.py → packages/aignostics/src/aignostics/__init__.py (replaces Phase 1 stub)

Codegen bundling fix

PYSDK-134 left a TODO about bundling codegen/out/aignx into the slim wheel (hatchling cannot reference paths outside the project root). Fixed by:

Created symlink packages/aignostics-sdk/src/aignx → ../../../codegen/out/aignx
Updated packages/aignostics-sdk/pyproject.toml: packages = ["src/aignostics_sdk", "src/aignx"]

Validation

uv sync --all-extras completes successfully
find src/ -name "*.py" | grep -v __pycache__ | grep -v codegen returns only src/aignostics.py (the PyInstaller launcher)
Symlink resolves: ls packages/aignostics-sdk/src/aignx/codegen/ shows codegen API files

Jira

PYSDK-135

Test plan

Verify uv sync --all-extras succeeds
Verify ls packages/aignostics-sdk/src/aignostics_sdk/ shows platform/, utils/, constants.py, __init__.py
Verify ls packages/aignostics/src/aignostics/ shows all domain modules
Verify ls packages/aignostics-sdk/src/aignx/codegen/ resolves through the symlink
Verify no Python source files remain in old src/aignostics/ location (except src/aignostics.py PyInstaller launcher)

- 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.

Copilot

Pull request overview

This PR advances the workspace package split by relocating source from the legacy src/aignostics/ layout into the new full aignostics and slim aignostics-sdk package directories. It also updates the slim package wheel configuration to include the generated aignx client package.

Changes:

Moves full-package domain modules, GUI assets, scripts, and constants into packages/aignostics/src/aignostics/.
Moves platform/client utilities into packages/aignostics-sdk/src/aignostics_sdk/.
Updates aignostics-sdk wheel packaging to include both aignostics_sdk and aignx.

Reviewed changes

Copilot reviewed 6 out of 145 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
`src/aignostics/__init__.py`	Removes legacy package initializer from old source tree.
`packages/aignostics/src/aignostics/__init__.py`	Restores full package boot initializer in new package location.
`packages/aignostics/src/aignostics/constants.py`	Adds full-package constants in new location.
`packages/aignostics/src/aignostics/cli.py`	Adds full-package CLI entry module.
`packages/aignostics/src/aignostics/application/__init__.py`	Adds application package exports.
`packages/aignostics/src/aignostics/application/_models.py`	Adds application progress models.
`packages/aignostics/src/aignostics/application/_settings.py`	Adds application settings.
`packages/aignostics/src/aignostics/application/_gui/_page_builder.py`	Adds application GUI route registration.
`packages/aignostics/src/aignostics/application/_gui/_page_index.py`	Adds application homepage GUI.
`packages/aignostics/src/aignostics/application/_gui/_utils.py`	Adds application GUI display helpers.
`packages/aignostics/src/aignostics/application/_gui/assets/*`	Moves application GUI image and animation assets.
`packages/aignostics/src/aignostics/bucket/__init__.py`	Adds bucket package exports.
`packages/aignostics/src/aignostics/bucket/_settings.py`	Adds bucket settings.
`packages/aignostics/src/aignostics/bucket/assets/Google-Cloud-logo.png`	Moves bucket GUI asset.
`packages/aignostics/src/aignostics/dataset/__init__.py`	Adds dataset package exports.
`packages/aignostics/src/aignostics/gui/__init__.py`	Adds GUI package exports.
`packages/aignostics/src/aignostics/gui/_error.py`	Adds GUI error page handling.
`packages/aignostics/src/aignostics/gui/_theme.py`	Adds GUI theme setup.
`packages/aignostics/src/aignostics/gui/CLAUDE.md`	Moves GUI module guidance.
`packages/aignostics/src/aignostics/notebook/__init__.py`	Adds notebook package exports.
`packages/aignostics/src/aignostics/notebook/_gui.py`	Adds notebook GUI page.
`packages/aignostics/src/aignostics/notebook/_notebook.py`	Adds bundled Marimo notebook.
`packages/aignostics/src/aignostics/qupath/__init__.py`	Adds QuPath package exports.
`packages/aignostics/src/aignostics/qupath/_gui.py`	Adds QuPath GUI page.
`packages/aignostics/src/aignostics/qupath/_settings.py`	Adds QuPath settings.
`packages/aignostics/src/aignostics/qupath/assets/*`	Moves QuPath GUI animation assets.
`packages/aignostics/src/aignostics/qupath/scripts/*.groovy`	Moves QuPath helper scripts.
`packages/aignostics/src/aignostics/system/__init__.py`	Adds system package exports.
`packages/aignostics/src/aignostics/system/_exceptions.py`	Adds system exception type.
`packages/aignostics/src/aignostics/system/_gui.py`	Adds system GUI page.
`packages/aignostics/src/aignostics/system/_settings.py`	Adds system settings.
`packages/aignostics/src/aignostics/system/assets/system.lottie`	Moves system GUI asset.
`packages/aignostics/src/aignostics/third_party/showinfm/**`	Moves vendored file-manager helper package.
`packages/aignostics/src/aignostics/wsi/__init__.py`	Adds WSI package exports.
`packages/aignostics/src/aignostics/wsi/_cli.py`	Adds WSI CLI commands.
`packages/aignostics/src/aignostics/wsi/_gui.py`	Adds WSI thumbnail/TIFF routes.
`packages/aignostics/src/aignostics/wsi/_service.py`	Adds WSI service implementation.
`packages/aignostics-sdk/pyproject.toml`	Updates slim wheel packages to include `aignx`.
`packages/aignostics-sdk/src/aignostics_sdk/__init__.py`	Updates slim package initializer.
`packages/aignostics-sdk/src/aignostics_sdk/constants.py`	Adds slim package constants.
`packages/aignostics-sdk/src/aignostics_sdk/platform/__init__.py`	Adds platform package exports.
`packages/aignostics-sdk/src/aignostics_sdk/platform/_api.py`	Adds authenticated API wrapper.
`packages/aignostics-sdk/src/aignostics_sdk/platform/_cli.py`	Adds platform CLI commands.
`packages/aignostics-sdk/src/aignostics_sdk/platform/_constants.py`	Adds platform constants.
`packages/aignostics-sdk/src/aignostics_sdk/platform/_messages.py`	Adds platform messages.
`packages/aignostics-sdk/src/aignostics_sdk/platform/_operation_cache.py`	Adds platform operation cache utilities.
`packages/aignostics-sdk/src/aignostics_sdk/platform/_utils.py`	Adds platform utility functions.
`packages/aignostics-sdk/src/aignostics_sdk/platform/resources/__init__.py`	Adds platform resources package marker.
`packages/aignostics-sdk/src/aignostics_sdk/platform/resources/utils.py`	Adds platform pagination helper.
`packages/aignostics-sdk/src/aignostics_sdk/utils/__init__.py`	Adds slim utility package exports.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_cli.py`	Adds CLI utility helpers.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_console.py`	Adds shared console setup.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_constants.py`	Adds runtime constants.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_di.py`	Adds discovery helpers.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_fs.py`	Adds filesystem helpers.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_health.py`	Adds health models.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_log.py`	Adds logging setup.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_mcp.py`	Adds MCP helpers.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_nav.py`	Adds GUI navigation helpers.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_notebook.py`	Adds notebook server helpers.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_process.py`	Adds process helpers.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_service.py`	Adds base service class.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_settings.py`	Adds settings utilities.
`packages/aignostics-sdk/src/aignostics_sdk/utils/_user_agent.py`	Adds user-agent helper.
`packages/aignostics-sdk/src/aignostics_sdk/utils/boot.py`	Adds boot sequence.


 [tool.hatch.build.targets.wheel]
-packages = ["src/aignostics_sdk"]
+packages = ["src/aignostics_sdk", "src/aignx"]


Copilot AI review requested due to automatic review settings May 28, 2026 11:04

ari-nz requested a review from a team as a code owner May 28, 2026 11:04

ari-nz added the skip:test:long_running Skip long-running tests (≥5min) label May 28, 2026

Copilot started reviewing on behalf of ari-nz May 28, 2026 11:05 View session

Copilot AI reviewed May 28, 2026

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Comment thread packages/aignostics-sdk/pyproject.toml

[tool.hatch.build.targets.wheel]

packages = ["src/aignostics_sdk"]

packages = ["src/aignostics_sdk", "src/aignx"]

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feat(packaging): migrate source into workspace package directories [PYSDK-135]#656

feat(packaging): migrate source into workspace package directories [PYSDK-135]#656
ari-nz wants to merge 1 commit into
feat/PYSDK-134/workspace-scaffoldingfrom
feat/PYSDK-135/source-migration

ari-nz commented May 28, 2026 •

edited

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ari-nz commented May 28, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Release Train — PYSDK-133

Summary

What moved where

→ packages/aignostics-sdk/src/aignostics_sdk/ (slim package)

→ packages/aignostics/src/aignostics/ (full package)

Codegen bundling fix

Validation

Jira

Test plan

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Pull request overview

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ari-nz commented May 28, 2026 •

edited

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→ `packages/aignostics-sdk/src/aignostics_sdk/` (slim package)

→ `packages/aignostics/src/aignostics/` (full package)