Address deferred review cleanup on staging

[alxndrkalinin]

Addressing issues leftover from integration of app-dynaclr and app-cytoland in #379 (comment)

Summary

• viscy-utils treated anndata and wandb as core dependencies even though they are only needed for optional evaluation and embedding-export workflows; this forced every consumer to install heavier packages unnecessarily. This PR moves them behind optional extras, keeps tensorstore core because it is still on the CLI import path, and declares viscy-data explicitly because the embedding callbacks import viscy_data at runtime.
• embedding snapshot code depended on the private EmbeddingWriter._collect_data_provenance() helper, and annotation.convert() both stacked xarray coords without explicit .data extraction and imported optional anndata/natsort at module import time. This PR exposes collect_data_provenance() as a public helper shared by both callbacks, makes the coordinate stacking explicit to avoid fragile xarray-to-numpy coercion, and lazy-imports the optional annotation dependencies with a clear runtime error only when conversion is invoked.
• dynaclr used deprecated nn.functional.sigmoid() in classification prediction. This PR replaces it with torch.sigmoid().
• dynaclr tests relied on a root-level pytest pythonpath hack so helpers.py could be imported as a top-level module, which leaked a test-only module into unrelated root test sessions. This PR folds the shared test helpers into conftest.py, updates imports, adds app-local pytest config for dynaclr, and removes the root pythonpath override so test setup stays local to the app.

[Copilot]

Pull request overview

This PR cleans up staging-related technical debt across the monorepo by tightening viscy-utils dependency metadata, exposing a shared provenance helper, improving xarray coordinate handling during annotation conversion, and removing a brittle pytest pythonpath leak in DynaCLR tests.

Changes:

• Refactor viscy-utils dependency/extras metadata (move anndata/natsort/wandb to extras; add viscy-data runtime dep) and expose collect_data_provenance as a public helper.
• Tighten xarray coordinate extraction in AnnData conversion and update callbacks to use the shared provenance helper.
• Make DynaCLR tests self-contained by inlining shared helpers into conftest.py, updating imports, and adding app-local pytest pythonpath; replace deprecated nn.functional.sigmoid usage.

Reviewed changes

Copilot reviewed 17 out of 18 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
uv.lock	Updates locked dependency/extras metadata for viscy-utils, including new viscy-data runtime dep and extras markers.
pyproject.toml	Removes root-level pytest pythonpath entry that leaked DynaCLR test paths globally.
packages/viscy-utils/pyproject.toml	Moves anndata to an extra, adds viscy-data runtime dep, and redefines extras/dev groups.
packages/viscy-utils/src/viscy_utils/evaluation/annotation.py	Uses .data for embedding coordinate stacking during xarray→AnnData conversion.
packages/viscy-utils/src/viscy_utils/callbacks/embedding_writer.py	Promotes data provenance extraction to a public helper and reuses it.
packages/viscy-utils/src/viscy_utils/callbacks/embedding_snapshot.py	Switches to the shared provenance helper.
applications/dynaclr/tests/helpers.py	Removes standalone helper module; functionality moved into conftest.py.
applications/dynaclr/tests/conftest.py	Inlines shared constants/helpers and keeps pytest config/fixtures in one place.
applications/dynaclr/tests/test_*.py	Updates imports to pull shared helpers/constants from conftest.
applications/dynaclr/src/dynaclr/classification.py	Replaces deprecated nn.functional.sigmoid with torch.sigmoid.
applications/dynaclr/pyproject.toml	Adds app-local pytest config (pythonpath = ["tests"]).

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[edyoshikun]

Sorry, we can remove 69a1e93 from this PR.

the other two commits were to remove some miscellaneous folders and files that were left over. I did have to explicitly add the CI the test applictations/*.

I had issues running uv run pytest from root.

[Copilot]

Pull request overview

Copilot reviewed 28 out of 34 changed files in this pull request and generated 2 comments.

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[alxndrkalinin]

Latest changes:

• Dropped 69a1e93 as out-of-scope WandB/training config commit.
• Lazy-imported wandb and anndata in linear_classifier.py** following the same pattern as the annotation.py fix already in this PR
• Eliminated all from conftest import across test files and replaced with inlined constants (via synth_dims/hcs_dims fixture dicts) and fixture factories for classes/functions. Removed pythonpath = ["tests"] from app configs and __init__.py from app test dirs. Moved constants to fixtures.
• Root uv run pytest now collects all packages and applications (852 tests in one invocation)
• Restored empty src/viscy/__init__.py because hatchling requires it for the wheel build target. Without it uv build fails.

All tests pass:

• Root uv run pytest: 848 passed, 6 skipped, 1 xfailed
• applications/dynaclr: 205 passed, 4 skipped
• applications/cytoland: 21 passed
• applications/qc: 15 passed

[alxndrkalinin]

@edyoshikun I fixed conftest issues and some other small inconsistencies, should be ready for review