chore: add Pixi, CI, pre-commit, contributor guides and PR template - #1
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Superseded: the disjoint per-theme split couldn't pass CI (shared ruff/build config + cross-theme tests). Replaced by a stacked set: a core base PR (tooling+perf, verified green) with thin imaging/model/docs PRs stacked on it. |
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…oupling (#10) * fix: resolve audit findings across data, models, metrics, and imaging Address the open items from the whole-repository audit (AUDIT.md): - augmentation: re-sample parameters each epoch via DataAugmentation.reset_state (#1) - checkpoint: load_state_dict warm-starts resized layers and keeps siblings (#2) - patching: Accumulator raises a typed PatchError instead of UnboundLocalError (#14) - scheduler: update_scheduler raises ConfigError on an empty schedule (#15) - metrics: declare ssim/fid/lpips extras and raise an actionable MeasureError (#16) - models: rebuild LinearVAE on a real LatentDistribution bottleneck (#17), set Adaptation requires_grad in __init__ (#18), label debug blocks and make Write's output path explicit (#19) - transform: reuse a persisted Crop box to skip the full-volume read (#10) - dicom: non-destructive writes and multi-frame / irregular-spacing detection - network/metrics: thread the GPU-index counter explicitly instead of os.environ - apps: document number_of_mc_dropout as a reserved future feature (#11) Add regression tests (patching, named_forward, audit fixes, DICOM hardening) and expand AUDIT.md / AGENTS.md to cover the whole repository. * feat: add validation_augmentations and zero-LR training stop Re-apply two drafted improvements onto the modernized core: - DataTrain gains a `validation_augmentations` flag (default true). When false, the train and validation datasets are prepared separately so augmented variants never leak into validation; the float split is now computed from per-case entry counts. `_get_validation_mapping()` is the single accessor that enforces this invariant. - EarlyStopping: move `early_stop`/`is_stopped` to `EarlyStoppingBase`, add `stop()`, and end the run cleanly once the schedulers decay the optimizer learning rate to <= 0. Also remove the now-dead `_split_train_validation` (replaced by `_split_train_validation_names`) and migrate its tests. The drafted SSIM index change was intentionally dropped: `MaskedLoss.forward` passes the full [B, C, ...] tensor, so the existing `x[0][0]` indexing is correct. Add unit tests for the disabled-validation-augmentation paths and for EarlyStopping, and document the new key in the examples, the training guide, and AGENTS.md. * refactor: decouple konfai-apps runtime deps from the core konfai-apps is an independent package: its runtime deps (fastapi, uvicorn, python-multipart) belong in konfai-apps/pyproject.toml, not in the core. Remove them from konfai's `[dev]` extra and the Pixi `dev` feature so `pip install konfai` no longer drags in the apps server stack; `pip install konfai-apps` (or `pip install -e ./konfai-apps`) pulls them itself. Re-lock pixi (drops fastapi/uvicorn/python-multipart + orphaned transitives) and document that the apps suite needs `pip install -e ./konfai-apps` first. The shared lint/format/bandit tooling stays (one config for the monorepo). Core is unchanged (it never imported these); the apps wheel stays self-contained (Requires-Dist: konfai, fastapi, uvicorn, python-multipart) and its 31 tests pass.
vboussot
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- AGENTS.md (303 -> 93 lines): a shorter, more general guide. Keeps the load-bearing parts -- the three design pillars, the extension model (subclass + classpath), the do-not-break invariants, and the coding/commit/ agent conventions -- and drops the verbose config-key catalogues, per-subsystem deep-dives, env-var/optional-dep tables, and the end-to-end run trace, which belong in docs/ and examples/. - AUDIT.md (206 -> 64 lines): rewritten to the current state after PR #10. It records concisely what is fixed (modernization #6-#9 + audit follow-up #1, #2, #10, #14-#19, DICOM hardening, os.environ device fix) versus what remains -- the audit does NOT claim everything is resolved: ~9 confirmed bugs are still a clearly-listed backlog (#3 VAE noise, #4 EMA early-stop score, #5 explicit Standardize, #6 Rotate deg->rad, #7 CLI tensorboard, #8 Unsqueeze, #9 ResampleToShape, #12 Select, #13 ITK) plus the deferred cross-cutting refactors.
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Description
Developer environment, CI, and contributor tooling.
itk,hdf5,dicom,omezarr,imaging,monitoring, ...).konfai_ci,pre-commit,commit-hygiene), pre-commit config, commit-message branding check.AGENTS.md,CLAUDE.md, copilot instructions), a development guide, installation docs, and a GitHub PR template.Testing
pixi run check— green.