ci: green up modular-viscy-staging (CI matrix, deps, lint)

[edyoshikun]

Summary

Restore green CI on modular-viscy-staging so PR #373 (the 0.5 merge to main) can land. Four atomic commits, each fixing one distinct failure class observed on the #373 CI run.

What's broken on modular-viscy-staging today

After pushing the merge commit to modular-viscy-staging, PR #373 ran CI for the first time and surfaced five pre-existing failure classes (none caused by the merge itself):

Failure	Job	Root cause
uv sync errors on Python 3.11	Test (3.11 matrix entries)	All workspace packages declare requires-python = ">=3.12". CI matrix still includes 3.11 → fail-fast: true cancels every 3.12/3.13 sibling.
ModuleNotFoundError: No module named 'viscy_transforms'	Test Data Extras	packages/viscy-data/tests/test_combined.py (+ 2 others) import viscy_transforms, but the test group does not declare it.
ModuleNotFoundError: No module named 'hydra'	Test dynacell benchmark configs	applications/dynacell/src/dynacell/evaluation/pipeline.py:9 imports hydra unconditionally, but hydra-core is gated behind the eval / report extras. CI installs with uv sync --group test only.
FileNotFoundError: /home/eduardo.hirata/.../test_2d_mip_mixed.parquet	Test (dynaclr)	applications/dynaclr/scripts/dataloader_inspection/test_2d_mip_augmentation.py is a Jupyter-style demo (# %% cells, hard-coded /home/eduardo.hirata/... path) named with the test_ prefix, so pytest collects and crashes on it.
ruff/format/EOF/D/E/NPY violations	Lint	5 files needed ruff format, .envrc missing trailing newline, 1 E741, 3 D100, 1 D102, 1 NPY002.

Commits in this PR

1. ci: drop Python 3.11 from matrix and trigger on modular-viscy-staging — .github/workflows/test.yml, .github/workflows/lint.yml. Removes 3.11 from the matrix, adds modular-viscy-staging to push/pull_request triggers so future PRs targeting the 0.5 staging branch run lint/test.
2. fix(deps): declare viscy-transforms test dep and hydra-core for dynacell — Promotes hydra-core>=1.2 to dynacell's base dependencies (it's imported unconditionally), adds viscy-transforms to viscy-data's test group. Regenerated uv.lock.
3. fix(dynaclr): rename test_2d_mip_augmentation.py to demo_; scope pytest to tests/ — Renames the demo script to demo_2d_mip_augmentation.py, adds testpaths = ["tests"] under [tool.pytest.ini_options] in applications/dynaclr/pyproject.toml so future demo scripts under scripts/ are not collected when CI invokes pytest from applications/dynaclr/.
4. style: satisfy pre-commit (ruff format, EOF, D100/D102, E741, NPY002) — Auto-fixes from uvx prek run --all-files plus the 7 manual lint fixes.

Test plan

• CI on this PR turns green (lint + all Test* jobs).
• Once merged, re-run CI on PR Staging VisCy Monorepo #373 — should now be CLEAN (no DIRTY conflicts, no red checks blocking merge).

[Copilot]

Pull request overview

Restores green CI for the modular-viscy-staging branch by aligning the CI Python matrix with the repo’s requires-python>=3.12, fixing missing runtime/test dependencies, preventing pytest from collecting demo scripts, and applying lint/format cleanups.

Changes:

• Update CI workflows to run on modular-viscy-staging and drop Python 3.11 from the test matrix.
• Fix dependency gaps (viscy-transforms in viscy-data test group; hydra-core as a base dep for dynacell) and refresh uv.lock.
• Prevent accidental pytest collection of demo scripts in dynaclr, plus ruff/format and small reproducibility tweaks in tests.

Reviewed changes

Copilot reviewed 16 out of 18 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
uv.lock	Lockfile regeneration reflecting updated dependency declarations.
packages/viscy-utils/tests/test_mp_utils.py	Makes the test deterministic via a seeded NumPy Generator API.
packages/viscy-utils/src/viscy_utils/precompute.py	Ruff-format cleanup (no functional intent apparent).
packages/viscy-utils/src/viscy_utils/normalize.py	Ruff-format cleanup (no functional intent apparent).
packages/viscy-utils/src/viscy_utils/evaluation/lca.py	Minor print formatting refactor for reports.
packages/viscy-utils/src/viscy_utils/evaluation/distance.py	Ruff-format cleanup (no functional intent apparent).
packages/viscy-data/src/viscy_data/channel_dropout.py	Adds module/method docstrings to satisfy docstring linting.
packages/viscy-data/pyproject.toml	Adds viscy-transforms to the test dependency group.
applications/qc/tests/conftest.py	Ruff-format cleanup in test fixture generation.
applications/dynaclr/src/dynaclr/data/tau_sampling.py	Adds module docstring to satisfy linting.
applications/dynaclr/scripts/plotting/plot_dim_reduct.py	Adds module docstring to satisfy linting.
applications/dynaclr/scripts/dataloader_inspection/demo_2d_mip_augmentation.py	Renames demo script and updates usage text to avoid pytest collection.
applications/dynaclr/pyproject.toml	Configures pytest testpaths to scope collection to tests/.
applications/dynacell/src/dynacell/celldiff_wrapper.py	Renames ambiguous loop variable (O → Ov) and minor formatting.
applications/dynacell/pyproject.toml	Promotes hydra-core to a base dependency to match unconditional import usage.
.github/workflows/test.yml	Drops Python 3.11 from matrix; runs CI for modular-viscy-staging.
.github/workflows/lint.yml	Runs lint CI for modular-viscy-staging.
.envrc	Adds trailing newline / fixes EOF formatting.

Comments suppressed due to low confidence (1)

applications/dynacell/pyproject.toml:50

• hydra-core is now a base dependency, but it’s still listed in optional-dependencies.eval and optional-dependencies.report. Consider removing it from those extras to avoid redundant declarations and keep the meaning of the extras clear (then regenerate uv.lock).

dependencies = [
  "hydra-core>=1.2",
  "lightning>=2.3",
  "monai",
  "omegaconf",
  "pydantic>=2",
  "viscy-data[mmap]",
  "viscy-models[celldiff]",
  "viscy-transforms",
  "viscy-utils",
]
optional-dependencies.eval = [
  "accelerate>=1.13",
  "aicsmlsegment",
  "aicssegmentation",
  "cellpose",
  "cubic==0.7.0a2",
  "dynaclr",
  "hydra-core>=1.2",
  "iohub",

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